There are various ways to cite TaxonWorks, products derived from the software, and communities supporting the software. Here we offer general guidelines and some specific examples.
TaxonWorks Community (2022) TaxonWorks [software]. Species File Group (maintainers, https://speciesfilegroup.org). Accessible at: https://github.com/SpeciesFileGroup/taxonworks
@misc{taxonworks_software,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {TaxonWorks [software]},
+ year = {2022},
+ url = {https://github.com/SpeciesFileGroup/taxonworks},
+}
+
TaxonWorks Community (2022) TaxonWorks [software, Version 0.29.0]. Species File Group (maintainers, https://speciesfilegroup.org). Accessible at https://github.com/SpeciesFileGroup/taxonworks/tree/v0.29.0
@misc{taxonworks_software_version_29,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {TaxonWorks [software, Version 0.29.0]},
+ year = {2022},
+ url = {https://github.com/SpeciesFileGroup/taxonworks/tree/v0.29.0},
+}
+
TaxonWorks Community (2022) TaxonWorks [documentation]. Species File Group (maintainers, https://speciesfilegroup.org). [Accessed yyyy/mm/dd] Accessible at https://docs.taxonworks.org
Additional citations, referencing other specific aspects of the project, are concievable, they should follow the examples above. For example they might reference:
The non-code, but digital (captured and available somewhere, e.g. Issue tracker), contributions to the TaxonWorks community (e.g. opening issues, adding help documentation, etc.)
The non-code, and not digital, contributions, e.g. people we talked with that gave us ideas (has to be captured somewhere, e.g. personal communications)
<who, "community" or "individuals>. <year>. <project title, as seen in TW> curated in TaxonWorks [software]. <optional maintainer statement>. Retrieved <date> at <url, e.g. https://sfg.taxonworks.org/api/v1>.
@misc{my_data_in_taxonworks,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {<Project title as seen in TW> curated in TaxonWorks [software]},
+ year = {2022},
+ note = {Retrieved <timestamp> at <url>}
+}
+
We recommend treating all contributors as authors rather than dividing up roles in the citation.
Reference DOI or other identifier if the data is published and one is available
Reference a HASH of the data if the data is upublished
Resolving these questions might help to provide additional context:
Are you citing a) some or b) all of the data (what)?
Was the data retrieved in a) real time or b) via an "archive" (when)?
Was the data retrieved a) via an API (e.g. a resource described by https://api.taxonworks.org), b) some public interface (e.g. a portal that uses https://github.com/SpeciesFileGroup/taxonpages) c) within a private version of TaxonWorks (best to archive these publically!) or d) in a post-publication archive (e.g. Zenodo) (how)?
McElrath TC, Thomas MC, & Yoshida T. 2021. Nomenclature of family Laemophloeidae extracted from Cucujoidea World Catalog curated in TaxonWorks [software]. Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
McElrath TC, Thomas MC, & Yoshida T. 2021. Nomenclature of family Laemophloeidae extracted from Cucujoidea World Catalog curated in TaxonWorks [software]. Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Universal Chalcidoidea Database Curators. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Accessed on Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Heraty, John; Woolley, Jim, et al. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Accessed on Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Heraty, John; Woolley, Jim, et al. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Species File Group (maintainers, https://speciesfilegroup.org). Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
TW offers many ways for the community to offer help, find answers, and welcome all to join in the collective commons centered around the needs of researchers.
Developers and users are almost always online to chat. Join us via TaxonWorks Gitter Chat. A Github, or linked account is required to chat. The channel is open for all to review and search. Or join us through our TaxonWorks Slack that is connected to the Gitter Chat.
Every Wednesday, the Species File Group hosts topic-specific meetings currently covering nomenclature, digitization, matrices/observations, technical input, and two open sessions. Questions of any sort are welcome there, regardless of topic. All are welcome.
Refers to a geographic distribution record for a taxon listed in a publication. It is “asserted” in the sense that the information is simply taken as given from the publication. If it is “original” it is the first record for that OTU in that place.
A prefix (buffered_) used to indicate verbatim text that is part of a CollectionObject record. Buffered fields are used TaxonWorks in a digitization workflow as the first step of transcribing labels, or images, to digital data. Buffered fields are write-once, they after addition they should not be changed, nor do they track changes to parsed values.
Fields prefixed in cached_ are auto-generated by TaxonWorks based on other values in the record and/or records related to the record. They are used as indicies for searching and for display purposes, particularly cached_<>_html values.
Something that appears similar at the outset (e.g. an Icon), but changes in behaviour or appearance given where and when it is encountered in the application.
In this context, we want to talk about and focus on data fidelity. While we often refer to data quality, we note that in reality, quality as a categorical goal proves quite hard to define. It's subjective and "it depends" on may other factors. With fidelity as the goal, we can seek to ensure the data are as fit as possible (e.g formatted as expected, compliant with relevant standards) and whose completeness can be better understood or visualized. With fidelity as the goal, others can then determine if said data are fit-for-use for their research / data management needs and questions. We recognize and appreciate this considered nuance in terminology as shared by Erica Krimmel at TaxonWorks Together 2024 in our Data Quality Round Table Conversation.
Typing a combination of keys to trigger a behaviour in the UI. Universal hot keys include concepts like ctrl-c for "Copy text to clipboard". TaxonWorks has numerous hot key combinations that speed tasks.
Identifiers distinguish instances, i.e. specific things. TaxonWorks supports many different types of identifiers, and multiple identifiers can be added to individual instances. Some identifier types map 1:1 with physical things like the catalog number attached to specimen in collections, others types are strictly digitial. Some identifiers are Global, some are Local. Global identifiers are those that come from well thought out systems that mint identifiers that are intended to be truly globally (universally) unique. Local identifiers have a user-defined Namespace (the fixed bit of the identifier that doesn't change across the identifier) and a value, which must be unique within that Namespace.
Used in context of tracing text in buffered fields to the verbatim fields include parsed out values. "Naïve" means we anticipate a very simple match, string to string, no fuzziness, no AI, etc.
A “namespace” is the abbreviation for a collection used in specimen accession numbers. For example, in the accession number label USNM 1234567, “USNM” is the namespace. It is not necessarily the same as a repository, as there may be multiple namespaces used by a given repository.
An "object" is an abstract term often used when referencing the representation of a data instance in code. For example, in the underlying code in TaxonWorks there are TaxonName objects, CollectingEvent objects, CollectionObject objects, People objects, etc. We also often speak of adding attributes to objects. In the case of TaxonWorks these additions are called DataAttributes and AlternateValues. In this case we are adding some description to our data-object, for example a name for a "body of water" attribute to our CollectingEvent, or an abbreviation for a term in the tihe title of a Source.
In TaxonWorks parsed values are the formalized representation of the data. For example the verbatim date "12.iv.1997" parsed into three fields in TaxonWorks: start_date_day (12), start_date_month (4), start_date_year (1997).
In TW the parent is the next higher taxon in which the taxon of interest is classified, for example, a genus for a species or a subfamily for a genus. By setting the parent, a curator controls how the classification will appear in TW. For example, for a small family in which subfamilies are not used, the parent of a genus may be a family. In other cases, the parent of a genus could be a tribe. This is determined by the curator. The complete taxonomic history of the taxon’s classification is recorded separately on the Browse Nomenclature screen.
An instance of TaxonWorks supports multiple projects. Each project may have one or more users. Data in one project are only accessible in that project -- with a couple of key strategic exceptions (e.g. "Community" data like source publications that are public, or people names) where data are shared across projects.
“Protonym” in TW refers to a name at the species, genus or family level in its first validly published form. It will always be associated with a literature citation, and it has an author and date, as spelled out by the rules of ICZN. You can think of it as occupying a unique niche in nomenclatural hyperspace. In cases of synonymy, the protonym is not the currently valid name. The currently valid protonym is indicated in many places in by a check mark. However, note that for species names in a taxonomic history, the check mark will indicate the original combination of the name rather than the current one.
A simple means to elegantly suggest changes to a website or code repository by editing a clone of that respository and then sending a message back to the origin that includes those changes. The changes can be considered by the maintainers of the original respostory and integrated, or not.
"Standard operating proceedure." In TaxonWorks this might be a project-specific way of doing things. In TaxonWorks you can assert that some or all of your data was derived from some process by annotating it with a Protocol annotation.
A reference to a digitization process in where all data are laid out for complete capture within an image. TaxonWorks uses stages that have areas defined to match specific types of data, for example "Catalog numbers", "Specimen", "Image registration".
Verbatim fields in TaxonWorks are a small set of CollectingEvent fields that contain parts of the Verbatim or Buffered values. For example given a label like:
USA:TX:Brazos Co.
+Lick Creek Park
+12.iv.1997
+M. Yoder, YPT
+
Then the TaxonWorks verbatim fields verbatim_locality would contain 'Lick Creek Park' and the verbatim_date would include 12.iv.1997.
More on the background of TaxonWorks. Who to contact with questions. Ongoing events. Concepts behind TaxonWorks data modelling, approach to development, and more.
+
+
+
diff --git a/assets/404.html-CxyMnPEA.js b/assets/404.html-CxyMnPEA.js
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index 00000000..6b0948ae
--- /dev/null
+++ b/assets/404.html-CxyMnPEA.js
@@ -0,0 +1 @@
+import{_ as t,c as e,o,a}from"./app-Bwgh_xIT.js";const n={},c=a("p",null,"404 Not Found",-1),l=[c];function s(_,r){return o(),e("div",null,l)}const d=t(n,[["render",s],["__file","404.html.vue"]]),h=JSON.parse('{"path":"/404.html","title":"","lang":"en-US","frontmatter":{"layout":"NotFound"},"headers":[],"git":{},"filePathRelative":null}');export{d as comp,h as data};
diff --git a/assets/annotation.html-CcgTmaLE.js b/assets/annotation.html-CcgTmaLE.js
new file mode 100644
index 00000000..1476070a
--- /dev/null
+++ b/assets/annotation.html-CcgTmaLE.js
@@ -0,0 +1 @@
+import{_ as e,c as t,o as a,b as o}from"./app-Bwgh_xIT.js";const i={},n=o('
TaxonWorks excels in annotating data. Tags, notes, custom data-attributes, citations, alternative value, confidence levels, attribution and more are all customizable by the user then usable to enrich and manage their projects.
TaxonWorks provides a nearly universally applicable set of "annotation" types that can be used on core and supporting data.
You're checking out TaxonWorks, it seems to have most of what you need, but the UI seems to be missing fields for key data that are critical to your project. See Data attributes
TaxonWorks maps its internal model to well over 50 Darwin Core fields automatically. In addition, users can add Controlled Vocabulary Terms that reference DarwinCore fields to further extend the data that can be exported. See Darwin core exportable URIs.
As part of your SOP you are constantly needing to make temporary small groups of data to review and modify.
In TaxonWorks you can filter and select objects by Tags (and many other similar things). Tags can be batch created, destroyed in mass, and used to dynamically grow and shrink matrices, group your data into stages of a workflow, indicate things "TODO", filter records, add objects to loans, and much more. See Tags.
In your project it's important to know (record a provenance trail) that some Observations came from one SOP, while others came from another. See Protocols.
The Manage controlled vocabular terms task is used to customize the types of annotations you want to use. Think of it as creating the Keywords that your linking to your records, or the new column that you're adding to your table of data (e.g. names, collection objects, or collecting events).
If you are a project administrator you can make new fields (see Data attributes below) appear in the UI in various places.
Create the "fields" (see Data attributes below) you need
Click Project (top right), then Preferences (top left)
Select the model you want the new fields to appear for (e.g. CollectionObject)
Check all fields that you want to appear as input fields. Note that this creates new form-fields, you can always access and create data-attributes through the radial annotator.
Fields will now appear in the UI where pertinent, notably the Comprehensive digitization task, the OTU quick forms radial, and the New collecting event task.
Attributes inputs (bottom left) displaying for selected Predicates
Many annotation types start with the creation of a controlled vocabulary term (CVT). This is done in the Manage controlled vocabulary terms task.
All CVTs must have 2 parts:
A name, or label - used to select the CVT in the interface, for display, etc.
A definition - don't assume that your label is understandable, now, or over time! Provide a definition so that others may interpret and apply this CVT term as your project intends it to be used.
A third attribute is the Uri. This attribute is used to assert that the CVT in your project means the same things as data used in others projects.
Think of DataAttributes as custom columns on your table. There are two types in TaxonWorks, "Import", and "Internal". The latter are created in the user-interface, the former are used in the documentation of bulk-data import, typically for bespoke datasets. DataAttributes are key-value pairs that reference a record (or object. They reference the object the attribute is being attached to, a type of CVT called a Predicate, and the value.
For example you might add a DataAttribute referencing a Predicate you created called "TownshipAndRange" with the value "Smithville" to a CollectingEvent.
TaxonWorks "knows" about certain DarwinCore fields that are not 1:1 mappable to its model. To add data to these fields, and have them export 1:1 (i.e. typing "Stuff; Things" results in "Stuff; Things" being exported into the field) to your DarwinCore exports do this:
Determine if the DwC attribute you want to use is "known" by TaxonWorks. At present it's best to do this by looking at the code itself, here is the list. If you find your attribute (e.g. asssociatedTaxa) then note (cpy to your clipboard) the URI it corresponds to (in our example http://rs.tdwg.org/dwc/terms/associatedTaxa).
In the Manage controlled vocabulary terms task create a new Predicate, name it typically 1:1 with the name of the DwC field, but this is required, the magic is in the Uri field.
Add the URI to your Predicate that you found in from the file above by pasting or typing it in.
You may want to add the field to directly to the UI, for example the New collecting event task or Comprehensive specimen digitization, see above for how to do this.
At this point you have a new field in TaxonWorks that will be exported to DwC when requested.
Note that on export no processing or validation is done on the export of these fields, you get in the export what you type in the field.
Tags are used an arbitrary label with your object. Think of tags as data attributes with no value. To create a type of Tag create a Keyword in the CVT manager. You can apply tags in the radial annotator, in batch in filter interfaces, and in various other ways.
Note that technically a Tag is the link (or join) between a Keyword (CVT) and an Object, not the Keyword itself.
Tagging an object with a Protocol asserts "some or all of the data in here came from this process. Create new protocols via Data->Protocols. You can attach PDFs describing your protocol to your Protocol to expand its description.
Alternate values reference a TaxonWorks field and provide a way to include a Translation, Abbreviation, Misspelling or Alternate spelling. To create one:
Open the radial annotator for the record in question
Select Alternate values
Select the type of alternate value (e.g. Abbreviation)
Select the target field (e.g. title of a source)
Add the value, and click Create.
Alternate values are not allowed on the name of a TaxonName, don't even think about requesting this.
Identifiers are broader subject (i.e. we need further discussion here). Briefly, there are two types in TaxonWorks, "Global", and "Local". The latter are in essence those types of identifiers that people thought really hard about, and tried to make universally applicable, the former, not so much.
In the real-world there are no-such-things as "unique" identifiers per object. TaxonWorks embraces this philosophy by allowing you to add as many identifiers to your data as you want. Identifiers can be used to say and do things like:
Conceptually, my digital thing is the same_as your digital thing
If you find my identifier you'll likely be able to find my thing (e.g. a Identifier::Local::CatalogNumber that represents a physical label localized_to my specimen)
The same things has two different "unique" identifiers, and that thing is my thing
I'm tracking (integrating/referencing/relating) this thing in my project, but with minimal detail, you can get more details on this thing if you can find other things "out there" with the same Identifier
My thing is the Person with this ORCiD (Identifier)
My thing historically could be found (your results may vary now) with this Identifier
I want to make labels for my specimens that reference my trip-codes so that I can quickly call them up, print them, assign them to Specimens, etc., and darn it my (Matt's) "MJY-YYYY" codes do not mean "Mark Jupiter Yahoo", but I need their (Mark's) "MJY" codes too. You can keep them the same, but different, using TaxonWorks' Namespaces.
Notes are the most unrestricted annotation type, you're simply adding a block of text (Markdown is allowed) to a record. You should not assume that all notes of are of some type. You should also not use Notes because you want something to appear somewhere, it's much better to do this with a more defined annotation such as a data attribute.
A Verifier is a very generic way of saying "This Person verified this record". It links a Person object with a role "verifier" to your data. There are no sub-types of verification, for that functionality see Confidences.
Some classes of data can be "documented", this simply means attaching a link to a binary document (e.g. pdf) to the record. The assertion being made is "this binary file contains the content of that thing", as in "This is the PDF of that Source".
Projects can create their own arbitrary levels of Confidence (think data-quality) that they can use to annotate there data with. For example you might have a ConfidenceLevel "1 - Origin unknonw" or "B - Spelling check required".
',65),r=[n];function s(l,d){return a(),t("div",null,r)}const h=e(i,[["render",s],["__file","annotation.html.vue"]]),u=JSON.parse(`{"path":"/guide/Manual/annotation.html","title":"Annotation","lang":"en-US","frontmatter":{"sidebarPosition":500},"headers":[{"level":2,"title":"Use cases","slug":"use-cases","link":"#use-cases","children":[{"level":3,"title":"My data don't fit in TaxonWorks!","slug":"my-data-don-t-fit-in-taxonworks","link":"#my-data-don-t-fit-in-taxonworks","children":[]},{"level":3,"title":"Export to a particular DarwinCore field","slug":"export-to-a-particular-darwincore-field","link":"#export-to-a-particular-darwincore-field","children":[]},{"level":3,"title":"I need to make a group of records","slug":"i-need-to-make-a-group-of-records","link":"#i-need-to-make-a-group-of-records","children":[]},{"level":3,"title":"I need to annotate this data with how it came to be","slug":"i-need-to-annotate-this-data-with-how-it-came-to-be","link":"#i-need-to-annotate-this-data-with-how-it-came-to-be","children":[]}]},{"level":2,"title":"User interface","slug":"user-interface","link":"#user-interface","children":[{"level":3,"title":"Radial annotator","slug":"radial-annotator","link":"#radial-annotator","children":[]},{"level":3,"title":"Manage controlled vocabulary terms task","slug":"manage-controlled-vocabulary-terms-task","link":"#manage-controlled-vocabulary-terms-task","children":[]},{"level":3,"title":"\\"Custom fields\\"","slug":"custom-fields","link":"#custom-fields","children":[]}]},{"level":2,"title":"Annotation types","slug":"annotation-types","link":"#annotation-types","children":[{"level":3,"title":"Controlled vocabulary terms","slug":"controlled-vocabulary-terms","link":"#controlled-vocabulary-terms","children":[]},{"level":3,"title":"Data attributes","slug":"data-attributes","link":"#data-attributes","children":[{"level":4,"title":"Customizing models","slug":"customizing-models","link":"#customizing-models","children":[]},{"level":4,"title":"Darwin Core exportable URIs","slug":"darwin-core-exportable-uris","link":"#darwin-core-exportable-uris","children":[]}]},{"level":3,"title":"Tags","slug":"tags","link":"#tags","children":[]},{"level":3,"title":"Protocols","slug":"protocols","link":"#protocols","children":[]},{"level":3,"title":"Alternate values","slug":"alternate-values","link":"#alternate-values","children":[]},{"level":3,"title":"Identifiers","slug":"identifiers","link":"#identifiers","children":[]},{"level":3,"title":"Notes","slug":"notes","link":"#notes","children":[]},{"level":3,"title":"Verifiers","slug":"verifiers","link":"#verifiers","children":[]},{"level":3,"title":"Documentation","slug":"documentation","link":"#documentation","children":[]},{"level":3,"title":"Confidences","slug":"confidences","link":"#confidences","children":[]}]}],"git":{"updatedTime":1682535910000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":2}]},"filePathRelative":"guide/Manual/annotation.md"}`);export{h as comp,u as data};
diff --git a/assets/api.html-D3B5XnWH.js b/assets/api.html-D3B5XnWH.js
new file mode 100644
index 00000000..0a171898
--- /dev/null
+++ b/assets/api.html-D3B5XnWH.js
@@ -0,0 +1 @@
+import{_ as a,c as e,o as i,b as n}from"./app-Bwgh_xIT.js";const t={},r=n('
Technically there are many APIs in TaxonWorks, however when we use the word in the context of TaxonWorks we almost always are doing so in reference to the functionality that lets you access your data outside the user-interfaces.
Very simply, the API lets you make a query on your data (and other's that have made it accessible), and returns you a response. It gives you "behind-the-scenes" access to the data the user interfaces are managing.
',6),o=[r];function s(c,p){return i(),e("div",null,o)}const h=a(t,[["render",s],["__file","api.html.vue"]]),d=JSON.parse('{"path":"/guide/api.html","title":"API","lang":"en-US","frontmatter":{"sidebarPosition":200},"headers":[{"level":2,"title":"An API is an application programing interface","slug":"an-api-is-an-application-programing-interface","link":"#an-api-is-an-application-programing-interface","children":[]}],"git":{"updatedTime":1678491307000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":3},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":2}]},"filePathRelative":"guide/api.md"}');export{h as comp,d as data};
diff --git a/assets/app-Bwgh_xIT.js b/assets/app-Bwgh_xIT.js
new file mode 100644
index 00000000..426d791a
--- /dev/null
+++ b/assets/app-Bwgh_xIT.js
@@ -0,0 +1,26 @@
+/**
+* @vue/shared v3.4.27
+* (c) 2018-present Yuxi (Evan) You and Vue contributors
+* @license MIT
+**//*! #__NO_SIDE_EFFECTS__ */function Tl(e,t){const n=new Set(e.split(","));return i=>n.has(i)}const _e={},an=[],et=()=>{},ca=()=>!1,Un=e=>e.charCodeAt(0)===111&&e.charCodeAt(1)===110&&(e.charCodeAt(2)>122||e.charCodeAt(2)<97),Ll=e=>e.startsWith("onUpdate:"),Le=Object.assign,Al=(e,t)=>{const n=e.indexOf(t);n>-1&&e.splice(n,1)},ua=Object.prototype.hasOwnProperty,he=(e,t)=>ua.call(e,t),ee=Array.isArray,cn=e=>Pi(e)==="[object Map]",_r=e=>Pi(e)==="[object Set]",oe=e=>typeof e=="function",Ae=e=>typeof e=="string",tn=e=>typeof e=="symbol",ke=e=>e!==null&&typeof e=="object",wr=e=>(ke(e)||oe(e))&&oe(e.then)&&oe(e.catch),xr=Object.prototype.toString,Pi=e=>xr.call(e),da=e=>Pi(e).slice(8,-1),Er=e=>Pi(e)==="[object Object]",Pl=e=>Ae(e)&&e!=="NaN"&&e[0]!=="-"&&""+parseInt(e,10)===e,un=Tl(",key,ref,ref_for,ref_key,onVnodeBeforeMount,onVnodeMounted,onVnodeBeforeUpdate,onVnodeUpdated,onVnodeBeforeUnmount,onVnodeUnmounted"),Ri=e=>{const t=Object.create(null);return n=>t[n]||(t[n]=e(n))},ha=/-(\w)/g,nt=Ri(e=>e.replace(ha,(t,n)=>n?n.toUpperCase():"")),fa=/\B([A-Z])/g,nn=Ri(e=>e.replace(fa,"-$1").toLowerCase()),qn=Ri(e=>e.charAt(0).toUpperCase()+e.slice(1)),Gi=Ri(e=>e?`on${qn(e)}`:""),$t=(e,t)=>!Object.is(e,t),Ki=(e,t)=>{for(let n=0;n{Object.defineProperty(e,t,{configurable:!0,enumerable:!1,writable:i,value:n})},ga=e=>{const t=parseFloat(e);return isNaN(t)?e:t},pa=e=>{const t=Ae(e)?Number(e):NaN;return isNaN(t)?e:t};let so;const Sr=()=>so||(so=typeof globalThis<"u"?globalThis:typeof self<"u"?self:typeof window<"u"?window:typeof global<"u"?global:{});function Gn(e){if(ee(e)){const t={};for(let n=0;n{if(n){const i=n.split(va);i.length>1&&(t[i[0].trim()]=i[1].trim())}}),t}function Ke(e){let t="";if(Ae(e))t=e;else if(ee(e))for(let n=0;nAe(e)?e:e==null?"":ee(e)||ke(e)&&(e.toString===xr||!oe(e.toString))?JSON.stringify(e,Lr,2):String(e),Lr=(e,t)=>t&&t.__v_isRef?Lr(e,t.value):cn(t)?{[`Map(${t.size})`]:[...t.entries()].reduce((n,[i,l],o)=>(n[Qi(i,o)+" =>"]=l,n),{})}:_r(t)?{[`Set(${t.size})`]:[...t.values()].map(n=>Qi(n))}:tn(t)?Qi(t):ke(t)&&!ee(t)&&!Er(t)?String(t):t,Qi=(e,t="")=>{var n;return tn(e)?`Symbol(${(n=e.description)!=null?n:t})`:e};/**
+* @vue/reactivity v3.4.27
+* (c) 2018-present Yuxi (Evan) You and Vue contributors
+* @license MIT
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This site contains the documentation.","sidebar":{"/develop/":[{"text":"Develop","link":"/develop/","children":["/develop/README.md","/develop/installation.md","/develop/contributing.md","/develop/bug-reporting.md","/develop/coding.md",{"text":"Data","link":"/develop/Data/","children":["/develop/Data/README.md","/develop/Data/models.md","/develop/Data/tables.md"]}]}],"/guide/":[{"text":"Guide","link":"/guide/","children":["/guide/README.md","/guide/start-a-project.md","/guide/migrate-to-TaxonWorks.md","/guide/getting-started.md",{"text":"Manual","link":"/guide/Manual/","children":["/guide/Manual/README.md","/guide/Manual/conventions.md",{"text":"Sources","link":"/guide/Manual/Sources/","children":["/guide/Manual/Sources/README.md"]},"/guide/Manual/collectionobject.md","/guide/Manual/collecting_event.md","/guide/Manual/digitization.md","/guide/Manual/matrices.md","/guide/Manual/identifiers.md","/guide/Manual/customization.md","/guide/Manual/nomenclature.md","/guide/Manual/annotation.md"]},"/guide/community-resources.md","/guide/data-quality.md","/guide/import.md","/guide/export.md","/guide/videos.md",{"text":"FAQs","link":"/guide/FAQs/","children":["/guide/FAQs/README.md"]},"/guide/api.md","/guide/other-documents.md"]}],"/about/":[{"text":"About","link":"/about/","children":["/about/README.md","/about/contact.md","/about/events.md","/about/citing-taxonworks.md","/about/glossary.md","/about/branding.md"]}]}},"/es/":{"lang":"es-ES","title":"Documentación de TaxonWorks","description":"TaxonWorks es un banco de trabajo con muchas herramientas para describir la vida. 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diff --git a/assets/branding.html-Cw6Z3OFd.js b/assets/branding.html-Cw6Z3OFd.js
new file mode 100644
index 00000000..773d2ad1
--- /dev/null
+++ b/assets/branding.html-Cw6Z3OFd.js
@@ -0,0 +1 @@
+import{_ as a,c as n,o as r,b as s}from"./app-Bwgh_xIT.js";const e="/images/branding/Logo-Full/TaxonWorks_Logo-Full-Black.svg",l="/images/branding/Logo-Full/TaxonWorks_Logo-Full-Brown.svg",o="/images/branding/Logo-Full/TaxonWorks_Logo-Full-Tan.svg",i="/images/branding/Logo-Full/TaxonWorks_Logo-Full-Green.svg",g="/images/branding/Logo-Full/TaxonWorks_Logo-Full-DarkGreen.svg",t="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-Black.svg",m="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-Brown.svg",c="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-Tan.svg",p="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-White.svg",b="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-Green.svg",d="/images/branding/Logo-Symbol/TaxonWorks_Logo-Symbol-DarkGreen.svg",_="/images/branding/Logo-Type/TaxonWorks_Logo-Type-Black.svg",y="/images/branding/Logo-Type/TaxonWorks_Logo-Type-Brown.svg",h="/images/branding/Logo-Type/TaxonWorks_Logo-Type-Tan.svg",k="/images/branding/Logo-Type/TaxonWorks_Logo-Type-White.svg",T="/images/branding/Logo-Type/TaxonWorks_Logo-Type-Green.svg",u="/images/branding/Logo-Type/TaxonWorks_Logo-Type-DarkGreen.svg",L={},x=s('
',10),f=[x];function v(S,W){return r(),n("div",null,f)}const w=a(L,[["render",v],["__file","branding.html.vue"]]),F=JSON.parse('{"path":"/about/branding.html","title":"Branding","lang":"en-US","frontmatter":{"sidebarPosition":70},"headers":[{"level":2,"title":"Logos","slug":"logos","link":"#logos","children":[{"level":3,"title":"Full","slug":"full","link":"#full","children":[]},{"level":3,"title":"Symbol","slug":"symbol","link":"#symbol","children":[]},{"level":3,"title":"Type","slug":"type","link":"#type","children":[]}]}],"git":{"updatedTime":1695173116000,"contributors":[{"name":"jlpereira","email":"pepelui@outlook.com","commits":2},{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"about/branding.md"}');export{w as comp,F as data};
diff --git a/assets/bug-reporting.html-Bt1RegO0.js b/assets/bug-reporting.html-Bt1RegO0.js
new file mode 100644
index 00000000..e7c9c2f7
--- /dev/null
+++ b/assets/bug-reporting.html-Bt1RegO0.js
@@ -0,0 +1 @@
+import{_ as e,c as i,o as r,b as t}from"./app-Bwgh_xIT.js";const o={},a=t('
Check to see that the issue is indeed new by carefully reviewing the existing issues.
While filing your issue:
Use a issue template if available, this categorizes your insights into more actionable items for those seeking to address it
Tell a story! Give us enough background so that we can replicate exactly what you did.
Include a success criterion. How do we know we've succeeded in addressing the issues without contacting you again?
Err on providing more, rather than less information.
Provide a meaningful title that identifies your role, and what you seek to accomplish, e.g. As an X I need Y to do Z
Some other conventions:
If you have the permissions, categorize your issue using a label.
Use the prefix "Task -" in the name to indicate the request for a new or improved task.
',10),s=[a];function n(l,u){return r(),i("div",null,s)}const c=e(o,[["render",n],["__file","bug-reporting.html.vue"]]),h=JSON.parse('{"path":"/develop/bug-reporting.html","title":"Bug reporting","lang":"en-US","frontmatter":{"sidebarPosition":40},"headers":[{"level":2,"title":"Considerations when reporting a bug or adding a feature request","slug":"considerations-when-reporting-a-bug-or-adding-a-feature-request","link":"#considerations-when-reporting-a-bug-or-adding-a-feature-request","children":[]}],"git":{"updatedTime":1668380273000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":3}]},"filePathRelative":"develop/bug-reporting.md"}');export{c as comp,h as data};
diff --git a/assets/bug-reporting.html-D9ecm319.js b/assets/bug-reporting.html-D9ecm319.js
new file mode 100644
index 00000000..4255e3f8
--- /dev/null
+++ b/assets/bug-reporting.html-D9ecm319.js
@@ -0,0 +1 @@
+import{_ as e,c as a,o,b as i}from"./app-Bwgh_xIT.js";const r={},s=i('
Verifique que el issue es nuevo revisando los issues existentes.
Mientras llene su issue:
Use un template de issue si está disponible, esto desglosa sus ideas en items mas accesibles para aquellos que buscan abordarlos
Cuenta una historia! Denos suficiente trasfondo para que podamos replicar exactamente lo que hizo.
Incluya un criterio exitoso. ¿Cómo sabemos que hemos conseguido resolver los problemas sin volver a ponernos en contacto con usted?
Es preferible dar mas información que menos.
Proporcione un titulo significativo que identifique su función y lo que pretende conseguir, por ejemplo: Como X necesito Y para hacer Z
Otras convenciones:
Si tiene permisos, categorice su issue utilizando una etiqueta.
Use el prefix "Task -" en el titulo para indicar la solicitud para una nueva tarea o mejorarla.
',10),t=[s];function n(u,c){return o(),a("div",null,t)}const p=e(r,[["render",n],["__file","bug-reporting.html.vue"]]),d=JSON.parse('{"path":"/es/develop/bug-reporting.html","title":"Reportar un bug","lang":"es-ES","frontmatter":{"sidebarPosition":40},"headers":[{"level":2,"title":"Consideraciones cuando reporte un bug o agregue una solicitud de característica.","slug":"consideraciones-cuando-reporte-un-bug-o-agregue-una-solicitud-de-caracteristica","link":"#consideraciones-cuando-reporte-un-bug-o-agregue-una-solicitud-de-caracteristica","children":[]}],"git":{"updatedTime":1677462190000,"contributors":[{"name":"jlpereira","email":"pepelui@outlook.com","commits":1}]},"filePathRelative":"es/develop/bug-reporting.md"}');export{p as comp,d as data};
diff --git a/assets/citing-taxonworks.html-DDur_T5C.js b/assets/citing-taxonworks.html-DDur_T5C.js
new file mode 100644
index 00000000..b6b58b81
--- /dev/null
+++ b/assets/citing-taxonworks.html-DDur_T5C.js
@@ -0,0 +1,37 @@
+import{_ as e,c as a,o as t,b as i}from"./app-Bwgh_xIT.js";const o={},n=i(`
There are various ways to cite TaxonWorks, products derived from the software, and communities supporting the software. Here we offer general guidelines and some specific examples.
TaxonWorks Community (2022) TaxonWorks [software]. Species File Group (maintainers, https://speciesfilegroup.org). Accessible at: https://github.com/SpeciesFileGroup/taxonworks
@misc{taxonworks_software,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {TaxonWorks [software]},
+ year = {2022},
+ url = {https://github.com/SpeciesFileGroup/taxonworks},
+}
+
TaxonWorks Community (2022) TaxonWorks [software, Version 0.29.0]. Species File Group (maintainers, https://speciesfilegroup.org). Accessible at https://github.com/SpeciesFileGroup/taxonworks/tree/v0.29.0
@misc{taxonworks_software_version_29,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {TaxonWorks [software, Version 0.29.0]},
+ year = {2022},
+ url = {https://github.com/SpeciesFileGroup/taxonworks/tree/v0.29.0},
+}
+
TaxonWorks Community (2022) TaxonWorks [documentation]. Species File Group (maintainers, https://speciesfilegroup.org). [Accessed yyyy/mm/dd] Accessible at https://docs.taxonworks.org
Additional citations, referencing other specific aspects of the project, are concievable, they should follow the examples above. For example they might reference:
The non-code, but digital (captured and available somewhere, e.g. Issue tracker), contributions to the TaxonWorks community (e.g. opening issues, adding help documentation, etc.)
The non-code, and not digital, contributions, e.g. people we talked with that gave us ideas (has to be captured somewhere, e.g. personal communications)
<who, "community" or "individuals>. <year>. <project title, as seen in TW> curated in TaxonWorks [software]. <optional maintainer statement>. Retrieved <date> at <url, e.g. https://sfg.taxonworks.org/api/v1>.
@misc{my_data_in_taxonworks,
+ author = {{TaxonWorks Community}},
+ organization = {Species File Group (maintainers, https://speciesfilegroup.org)},
+ title = {<Project title as seen in TW> curated in TaxonWorks [software]},
+ year = {2022},
+ note = {Retrieved <timestamp> at <url>}
+}
+
We recommend treating all contributors as authors rather than dividing up roles in the citation.
Reference DOI or other identifier if the data is published and one is available
Reference a HASH of the data if the data is upublished
Resolving these questions might help to provide additional context:
Are you citing a) some or b) all of the data (what)?
Was the data retrieved in a) real time or b) via an "archive" (when)?
Was the data retrieved a) via an API (e.g. a resource described by https://api.taxonworks.org), b) some public interface (e.g. a portal that uses https://github.com/SpeciesFileGroup/taxonpages) c) within a private version of TaxonWorks (best to archive these publically!) or d) in a post-publication archive (e.g. Zenodo) (how)?
McElrath TC, Thomas MC, & Yoshida T. 2021. Nomenclature of family Laemophloeidae extracted from Cucujoidea World Catalog curated in TaxonWorks [software]. Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
McElrath TC, Thomas MC, & Yoshida T. 2021. Nomenclature of family Laemophloeidae extracted from Cucujoidea World Catalog curated in TaxonWorks [software]. Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Universal Chalcidoidea Database Curators. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Accessed on Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Heraty, John; Woolley, Jim, et al. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Accessed on Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
Heraty, John; Woolley, Jim, et al. 2022. Universal Chalcidoidea Database (UCD) curated in TaxonWorks [software]. Species File Group (maintainers, https://speciesfilegroup.org). Retrieved Oct 26, 2021 at https://sfg.taxonworks.org/api/v1/.
`,32),s=[n];function r(l,c){return t(),a("div",null,s)}const p=e(o,[["render",r],["__file","citing-taxonworks.html.vue"]]),h=JSON.parse('{"path":"/about/citing-taxonworks.html","title":"Citing TaxonWorks","lang":"en-US","frontmatter":{"sidebarPosition":40},"headers":[{"level":2,"title":"Software","slug":"software","link":"#software","children":[{"level":3,"title":"Collective code, documentation and API related material","slug":"collective-code-documentation-and-api-related-material","link":"#collective-code-documentation-and-api-related-material","children":[]},{"level":3,"title":"Code (version free)","slug":"code-version-free","link":"#code-version-free","children":[]},{"level":3,"title":"Code at a specific version","slug":"code-at-a-specific-version","link":"#code-at-a-specific-version","children":[]},{"level":3,"title":"Documentation (these pages)","slug":"documentation-these-pages","link":"#documentation-these-pages","children":[]},{"level":3,"title":"Other","slug":"other","link":"#other","children":[]}]},{"level":2,"title":"Data","slug":"data","link":"#data","children":[{"level":3,"title":"General citation guidance","slug":"general-citation-guidance","link":"#general-citation-guidance","children":[]},{"level":3,"title":"Other","slug":"other-1","link":"#other-1","children":[]}]},{"level":2,"title":"Other guidelines","slug":"other-guidelines","link":"#other-guidelines","children":[]},{"level":2,"title":"Additional examples","slug":"additional-examples","link":"#additional-examples","children":[]}],"git":{"updatedTime":1668384205000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":6},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":4}]},"filePathRelative":"about/citing-taxonworks.md"}');export{p as comp,h as data};
diff --git a/assets/coding.html-4yeWtbKl.js b/assets/coding.html-4yeWtbKl.js
new file mode 100644
index 00000000..25496e85
--- /dev/null
+++ b/assets/coding.html-4yeWtbKl.js
@@ -0,0 +1 @@
+import{_ as t,c as n,o as a,a as e,d as o}from"./app-Bwgh_xIT.js";const i={},s=e("h1",{id:"coding",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#coding"},[e("span",null,"Coding")])],-1),c=e("p",null,[e("em",null,[o("You "),e("em",null,"can"),o(" code (TaxonWorks). Here's where to learn how.")])],-1),d=e("p",null,[e("strong",null,"This page is a stub")],-1),l=[s,c,d];function r(m,_){return a(),n("div",null,l)}const p=t(i,[["render",r],["__file","coding.html.vue"]]),u=JSON.parse('{"path":"/develop/coding.html","title":"Coding","lang":"en-US","frontmatter":{"sidebarPosition":50},"headers":[],"git":{"updatedTime":1668380273000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":2}]},"filePathRelative":"develop/coding.md"}');export{p as comp,u as data};
diff --git a/assets/collecting_event.html-B7s0zL9d.js b/assets/collecting_event.html-B7s0zL9d.js
new file mode 100644
index 00000000..6a3842e3
--- /dev/null
+++ b/assets/collecting_event.html-B7s0zL9d.js
@@ -0,0 +1 @@
+import{_ as e,c as t,o as a,b as c}from"./app-Bwgh_xIT.js";const n={},l=c('
Exact - Return all records that have this, and only this, geographic area selected. Searches on CollectingEvent#geographic_area_id.
Descendants - Return all records that have the geographic area(s) or their descendants selected. Searches on CollectingEvent#geographic_area_id and GeograpihcArea#parent_id.
Spatial - If the geographic area has a shape tied to it this is permitted. Combine the results of the Descentants search and a spatial search referencing Georeferences and return all records that match either. In additions to fields in Descendants also does a spatial search on GeographicItem#<shape or point> as linked through Georeference#geographic_item_id and further to Collecting event via Georeference#collecting_event_id.
',9),i=[l];function o(r,s){return a(),t("div",null,i)}const h=e(n,[["render",o],["__file","collecting_event.html.vue"]]),g=JSON.parse('{"path":"/guide/Manual/collecting_event.html","title":"Collecting Events","lang":"en-US","frontmatter":{"sidebarPosition":205},"headers":[{"level":2,"title":"Collecting event related tasks","slug":"collecting-event-related-tasks","link":"#collecting-event-related-tasks","children":[{"level":3,"title":"Filter collecting events","slug":"filter-collecting-events","link":"#filter-collecting-events","children":[{"level":4,"title":"Facets","slug":"facets","link":"#facets","children":[{"level":5,"title":"Geographic area","slug":"geographic-area","link":"#geographic-area","children":[]}]}]}]}],"git":{"updatedTime":1711730288000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":2}]},"filePathRelative":"guide/Manual/collecting_event.md"}');export{h as comp,g as data};
diff --git a/assets/collectionobject.html-PgkJVJ26.js b/assets/collectionobject.html-PgkJVJ26.js
new file mode 100644
index 00000000..90117fcf
--- /dev/null
+++ b/assets/collectionobject.html-PgkJVJ26.js
@@ -0,0 +1 @@
+import{_ as e,c as o,o as t,b as i}from"./app-Bwgh_xIT.js";const a={},n=i('
A place for information about specimens and related collection items.
As a researcher, as an ecologist, as a collection manager, you want to gather, access, learn from, manage, (and later, share) data describing the Collection Objects (CO) that you steward. Inside TaxonWorks the CollectionObject model offers you a rich set of concepts and the ability to add custom Data Attributes as needed to store and share more data.
New collection object Task: This task suits digitization data capture workflows designed to support use of stub or skeletal records. Minimal data captured here, including text blocks, can be parsed later.
The New collection object task best suits minimal or skeletal data record creation
New Collecting Event Task: In addition to the data about the what (that is, the physical specimen itself), information about the where, how, who, and when, etcetera fit in the TaxonWorks data model in the New Collecting Event (CE) Task.
Use the New collecting event task to capture events
Comprehensive specimen digitization Task (CSD): Combined into one screen, much of the data you have related to a specimen can be entered inside this one window. Inside this task, you have access to buffered data from stub records and verbatim data that can be parsed for you. You'll find you can add people, locality information, biological association data, and add custom fields you need. The following screenshot highlights the different sections of this task in TaxonWorks.
Exploring the Comprehensive Digitization Task in TaxonWorks
In the top right of the above screenshot, note the options to change the layout of the Comprehensive specimen digitization task. Using these options, you can hide some content if not wanted or needed and move fields into a more optimum order for your data capture strategy.
In the top section of the CSD screenshot, you see sections for Catalog number, Repository, Preparation, Buffered, and Depictions.
Catalog number: TW provides several ways for you to add Catalog numbers to ensure you can find or subset your CO items as needed. Note the Namespace concept in TW which keeps Catalog numbers unique inside a TW Project.
Select an existing Namespace for this CO or add a New one if needed
You can Search to find the one you want.
Recent offers you items you've selected not too long ago.
Pinboard gives you the option to attach a given Namespace to the foreseeable items you plan to add at the moment.
Add your Catalog number identifier.
Check the increment box if you want to create records with numbers that increase accordingly.
Repository: Search for the place where the specimen resides.
Use Quick to search using a few letters to find the place.
With Recent option you can make us of the last entries made if you might be entering data for items being cared for at the same insitutions.
The Pinboard option lets you pick an option (for quick easy access) to be there always unless you remove it from the pinboard.
Preparation: Select the storage method type from options shown. Note you can add to this list if need be as follows.
Navigate to the Data tab
Search for Preparation types and click on the result
In the Preparation types window, click New
Type in the name of the method
Type the definition of what this term means.
ClickCreate Preparation type
Buffered: Information here can be typed in OR might come from a different task in TaxonWorks that involves capturing an image of labels (and specimens) and getting label text from either typing or from OCR. Data in these fields is not expected to change or be edited.
Depictions: Drag and drop any relevant media (images or figures) into this box.
Here you find the information about the who, when, and where for the specimen collected. Note this is a separate task in TW. (See New Collecting Event (CE) Task ). The CE fields offered here make it easier to enter all relevant information in one window, in one task. Note the CE has 3 columns, Verbatim, Parse, and then label printing and locality preview.
Verbatim Collecting Event column
Label: Enter data here from the label.
You may wish to try Parse fields for the software to help you move the label text into the correct atomized fields.
Locality: Enter verbatim information from the label or other source describing where on the planet this specimen was collected.
Latitude: if provided on label or in another related souce, enter the latitude as it is shown in the image or relevant document.
Longitude: if provided on label or in another related souce, enter the longitude as it is shown in the image or relevant document.
Geolocation uncertainty in meters: a number expected to already to be meters
Elevation: if provided on label or in another related souce, enter the elevation as it is shown in the image or relevant document.
Habitat: if provided on label or in another related souce, enter the habitat as it is shown in the image or relevant document.
Date: if provided on label or in another related souce, enter the date as it is shown in the image or relevant document.
Datum: if provided on label or in another related souce, enter the datum as it is shown in the image or relevant document.
Collectors: if provided on label or in another related souce, enter the collectors as they appear in the image or relevant document. This would have the collector information as it appears on your document.
Method: if provided on label or in another related souce, enter the method as it is shown in the image or relevant document.
Trip identifier: if provided on label or in another related souce, enter this identifier as it is shown in the image or relevant document.
Parse section of CE This section helps to atomize all the information about when and where and who into separate bits of information. Some features offered here include tools to help you georeference, to indicate units of measurement, and to auto-parse data from the Verbatim information.
Geographic area: Search to find the desired higher-level geography (e. g. State, or Country). Again (as above) you have options to use Quick, Recent, or Pinboard to speed finding the place. Additionally, you can use Map and then click on the desired place in the resulting map presented.
Note that you may find multiple options offered to you. Example, for Alabama, we are offered 4 choices (from various gazetteers). Some are used by many specimens. Choose the one that seems correct (or as outlined by your Project needs documentation).
Start date: Enter the start date (YYYY MM DD)
End date: Enter the end date (YYYY MM DD) for the CE
Elevation: note a range and uncertainty can be added here. Please declare the units.
Start time: If relevant and provided, enter the time the event started.
End time: If relevant and provided, enter the time the event ended.
Collectors section: Search to find the collector(s). Click the desired Collector from the drop-down list. If you have more than one, Search to find the next collector and again, Click the desired name from the drop-down list. If the name you are searching for is not there, type the name (family name, given name) and Clickadd new. Repeat until you have all the collectors added for that Collecting Event.
Trip code section: The trip code comes from the combination of a Namespace and an Identifier. Together, they server as your unique identifier you assigned to this Collecting Event.
Namespace : Search to find the desired Namespace (if desired). You may need to add a Namespace. To do that see New namespace task.
Identifier: Enter the alphanumeric value that was selected for this Collecting Event.
Group: This is a geological term. From Wikipedia, "a lithostratigraphic unit consisting of a series of related formations that have been classified together to form a group." Enter the Group name.
Formation: The full name of the lithostratigraphic formation from which the dwc:MaterialEntity was collected sensuDarwin Core dwc:formation
Member: The full name of the lithostratigraphic member from which the dwc:MaterialEntity was collected sensuDarwin Core:dwc:member
Lithology: From Wikipedia, "the lithology of a rock unit is a description of its physical characteristics visible at outcrop, in hand or core samples, or with low magnification microscopy." Enter the rock description here.
Minumum MA: The value representing an estimation for the minimum age of the material in million year units. MA is "megaannus".
Maximum MA: The value representing an estimation for the maximum age of the material in million year units.
Custom attributes section: Each project in TaxonWorks can add new (customized) fields to their Collecting Events or their Collection Objects. Examples might be: -WaterBody: The name of the water body in which the dcterms:Location occurs. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:waterBody -georeferenceSources: A list (concatenated and separated) of maps, gazetteers, or other resources used to georeference the dcterms:Location, described specifically enough to allow anyone in the future to use the same resources. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:georeferenceSources -lowestBiostratigraphicZone: The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the dwc:MaterialEntity was collected. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:lowestBiostratigraphicZone.
To add new fields to either your CollectingEvent or CollectionObject data model, you will need to access
the Manage Controlled Vocabulary Terms task and
(For Project Administrators), the Project Preferences to associate the newly added terms with the correct TW Object (e. g. the CollectionObject or CollectingEvent) so these terms will appear in the relevant tasks.
Those using TW often create their own software manuals. They also produce customized workflows, protocols and procedures for specific tasks. Here, everyone can share access, input, and curation for these products.
Help Documentation from UCD@TW The Universal Chalcidoidea Database (UCD) Project in TW shares their manual with detailed instructions for using TaxonWorks to collectively manage nomenclatural and related taxonomic information for this group. Currently at version 2-19.
Guide to using filters in TaxonWorks The OSF community shares this manual to help all of us learn how to use the filters in TaxonWorks (e. g. Filter Nomenclature, Filter Sources, Filter CollectionObjects, Filter OTUs). Much of this how-to use filters will find its way into the shared cross-project documentation. Contact María Belén Cabrera mabecabrera at yahoo.com.ar to contribute and for questions.
Guide to INHS TaxonWorks Tasks This guide is very much a work in progress, and is intermittently uploaded, mostly by TC McElrath (contact monotomidae at gmail.com) for questions or if you have any comments.
',10),i=[s];function n(l,c){return a(),o("div",null,i)}const u=e(r,[["render",n],["__file","community-resources.html.vue"]]),h=JSON.parse('{"path":"/guide/community-resources.html","title":"Community Documentation","lang":"en-US","frontmatter":{"sidebarPosition":50},"headers":[{"level":2,"title":"Manuals","slug":"manuals","link":"#manuals","children":[{"level":3,"title":"Universal Chalcidoidea Database (UCD) Project","slug":"universal-chalcidoidea-database-ucd-project","link":"#universal-chalcidoidea-database-ucd-project","children":[]},{"level":3,"title":"Orthoptera Species File (OSF) Community","slug":"orthoptera-species-file-osf-community","link":"#orthoptera-species-file-osf-community","children":[]}]},{"level":2,"title":"Workflows","slug":"workflows","link":"#workflows","children":[{"level":3,"title":"INHS Insect Collection Standard Operating Procedures (SOPS)","slug":"inhs-insect-collection-standard-operating-procedures-sops","link":"#inhs-insect-collection-standard-operating-procedures-sops","children":[]}]}],"git":{"updatedTime":1695167580000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":1},{"name":"Deborah Paul","email":"dlpaul@illinois.edu","commits":1},{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"guide/community-resources.md"}');export{u as comp,h as data};
diff --git a/assets/contact.html-DcLCm-PO.js b/assets/contact.html-DcLCm-PO.js
new file mode 100644
index 00000000..d9670fde
--- /dev/null
+++ b/assets/contact.html-DcLCm-PO.js
@@ -0,0 +1 @@
+import{_ as e,c as t,o as a,b as o}from"./app-Bwgh_xIT.js";const n={},s=o('
TW offers many ways for the community to offer help, find answers, and welcome all to join in the collective commons centered around the needs of researchers.
Developers and users are almost always online to chat. Join us via TaxonWorks Gitter Chat. A Github, or linked account is required to chat. The channel is open for all to review and search. Or join us through our TaxonWorks Slack that is connected to the Gitter Chat.
TaxonWorks users frequent the Chat, and TaxonWorks events.
',8),r=[s];function i(c,l){return a(),t("div",null,r)}const p=e(n,[["render",i],["__file","contact.html.vue"]]),u=JSON.parse('{"path":"/about/contact.html","title":"Contact","lang":"en-US","frontmatter":{"sidebarPosition":10},"headers":[{"level":2,"title":"Chat","slug":"chat","link":"#chat","children":[]},{"level":2,"title":"Species File Group Community Liason","slug":"species-file-group-community-liason","link":"#species-file-group-community-liason","children":[]},{"level":2,"title":"Connect with TaxonWorks Users","slug":"connect-with-taxonworks-users","link":"#connect-with-taxonworks-users","children":[]}],"git":{"updatedTime":1676560206000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":2},{"name":"mjy","email":"diapriid@gmail.com","commits":2}]},"filePathRelative":"about/contact.md"}');export{p as comp,u as data};
diff --git a/assets/contributing.html-CroaaUjK.js b/assets/contributing.html-CroaaUjK.js
new file mode 100644
index 00000000..a1a7b931
--- /dev/null
+++ b/assets/contributing.html-CroaaUjK.js
@@ -0,0 +1,33 @@
+import{_ as e,c as a,o,b as n}from"./app-Bwgh_xIT.js";const t={},i=n(`
Primeramente, queremos agradecerle por esta tarea complicada. Interfaces (Por ejemplo, formularios, reportes, busquedas) los mockups son formas graficas de pedir por nuevas funcionalidades. Nos encanta verlos. Para crear un mock-up puede utilizar herramientas como Illustrator, Photoshop, o herramientas mas sofisticadas para este fin como Adobe XD, Pencil, Figma o Sketch, o simplemente puede dibujarla en un papel y tomarle una fotografia con su telefono. Los issue templates tienen campos para procesar imagenes, simplemente arrastrelas a la ventana y sueltelas allí. Escriba una pequeña historia de caso de uso, o agregue multiples imagenes que ayuden a describir como podrias utilizar esta interfaz.
Envielo! Es muy util que nos envie una grabación de su pantalla, o posicione la camara para que capture su trabajo en panalla y su entorno. Puede enviarnos los videos a traves de servicios como http://www.dropsend.com/. Busque la forma de contactarnos aqui
Varios archivos README.md existen en el codigo base.
Tenemos un linter de codigo(Rubocop), pero no es muy utilizado. Con el crecimiento esto podria cambiar. Tambien utilizamos ESLint para nuestro ecosistema de JavaScript moderno.
Este software junto a su flujo de trabajo hacen posible para todos contribuir a TaxonWorks Doc. Notese que todas las paginas aquí en docs.taxonworks.org tienen la funcionalidad de "Edita esta pagina en GitHub". Scrollea abajo del todo para verla.
NOTA: Usando este metodo también se garantiza que todos obtengan crédito y reconocimiento de contribución junto con la posibilidad de generar métricas y realizar un seguimiento de su trabajo.
Haga click en Commit changes para hacer un "pull request."
Rellene los campos utilizando el idioma ingles.
Agregue una muy breve descripción de sus cambios en el campo de texto que tiene Update ...
Opcionalmente, si lo desea, agregue una descripción mas larga en el campo de texto mas grande.
En su mensaje no utilice palabras como "Changed, tweaked, updated", describa que cosa fue hecha.
Elija la segunda opción Create a new branch .... Hay una excepción a esto, si sus cambios fueron pequeños y están listos para ir directo al sitio publico, entonces puede realizar un commit directamente a la rama development.
Haga click en Commit changes nuevamente.
Un miembro del repositorio de TaxonWorks Docs lo revisará, hará ediciones, le hará preguntas de ser necesario, y luego aceptará el pull request para fusionarlo en la documentación.
Al momento de decidir en que rama hacer el cambio, comience preguntándose: "¿Mi cambio está listo para publicarse ahora mismo?". Si la respuesta es si(Y tiene permisos), entonces puede hacer un commit a la rama development. Si la respuesta es no (Por ejemplo, quiere refinar aun mas el texto), entonces debería hacer el commit a una rama nueva.
Adicionalmente:
La rama development es el escenario de la rama main.
Siempre debe asumir que la rama development será publicada en cualquier momento.
Los cambios en development pueden acumularse antes de moverse a main.
La rama main nunca debe commitearse directamente. Los cambios a la rama main suceden cuando la rama development es funcionada dentro de esta.
Siempre es mas seguro y esta bien comenzar una rama nueva.
Siempre es mejor limitar el limite de tus cambios en cada nueva rama.
Si tiene una larga lista de cambios en su rama es util comenzar su session de edición funcionando development dentro de su rama de trabajo. Esto mantiene las diferencias entre development y su rama al mínimo.
Si está editando localmente, asegúrese de sincronizar sus cambios con los del servidor remoto (gil pull) antes de comenzar su session de edición.
Agregando documentación, notará que en todas las paginas de docs.taxonworks.org puede hacer un click en el icono del pincel para agregar/editar el texto. Para manejar los archivos de imagenes que agregamos a la documentación, utilizamos TaxonWorks Meta Project alojado en sfg.taxonworks.org. Para agregar imágenes a este, envíe un correo electrónico a dlpaul ARROBA illinois PUNTO edu o escribanos a traves de gitter. Cuando tome capturas de pantalla, tenga en cuenta que la resolución del monitor de su computadora marca la diferencia si estas imágenes son nítidas y claras o están pixeladas.
Tome las capturas de pantalla deseadas.
Suba esas imágenes(Todas o una por ves) a TaxonWorks Meta Project usando la tarea New Image.
En taxonWorks, busque el link de la imagen generada utilizando la tarea Filter Image. Utilice la faceta Housekeeping para limitar los resultados buscando las imágenes subidas por usted.
En el set resultante, haga click en la imagen deseada
Haga click en el Navegador radial debajo de la imagen y seleccione Show.
En Attributes copie el short URL to original URL link.
Vuelva a la edición de la documentación y use el formato markdown o HTML debajo para insertar las imágenes (Los ejemplos se encuentran debajo).
Note que ambos métodos permiten especificar el tamaño de la imagen
Los ejemplos aqui muestran en formato Markdown(md) como agregar una imagen con subtitulo.
Seleccione una de las cuatro opciones debajo para su subtitulo. Ponga esa linea de texto dentro de la documentación como texto descriptivo.
Con la opción position, elija left, center, o right para alinear el subtitulo de acuerdo a la opción elegida.
Escriba el texto de su elección dentro de los corchetes [el texto del subtitulo va aquí]
Peguelo en el short URL to original URL link (Desde Filter Image > Navegador radial > Show > Attributes).
Agregue el texto alt dentro de los corchetes, es buena practica incluirlo para accesibilidad.
(Opcional) Declare el ancho y alto o ambas de la imagen para controlar el tamaño en el que se mostraran.
El tamaño por defecto funciona bien. Algunas veces dependiendo de la captura de pantalla podría aparecer muy larga y entonces esta opción permite la opción de modificar su tamaño.
#position[caption text goes here](link [alt text if you want it])
+#position[caption text goes here](link [alt text if you want it] w{60%})
+#position[caption text goes here](link [alt text if you want it] h{50%})
+#position[caption text goes here](link [alt text if you want it] w{80%} h{50%})
+
Después de hacer un fork al repositorio, puede utilizar Github directamente para agregar un archivo. También puede agregar un archivo nuevo dentro de la interfaz de GitHub.
Unicamente en los archivos README.md. Utilícelo cuando quiera cambiar la posición del directorio dentro del contexto de otros directorios y archivos a nivel de ese directorio.
Por defecto, el sistema tomará los archivos dentro del directorio y los ordenará por alfabetico segun el nombre del archivo para generar el menu lateral. Por ejemplo:
Estructura de carpeta:
-- Mi carpeta de ejemplo
+---- bar.md
+---- foo.md
+
sidebarPosition permite que cambie el orden del menu lateral independientemente del orden alfabético de los archivos. Tomemos el ejemplo de arriba, pero ahora vamos a agregar sidebarPosition en cada archivo para cambiar su orden:
Nombre de archivo: foo.md
---
+sidebarPosition: 200
+---
+# A es la primera letra de este titulo
+
Nombre de archivo: bar.md
---
+sidebarPosition: 100
+---
+# B es la primera letra de este titulo
+
Para escribir la documentación utilizamos Markdown. Existen muchas guías sobre como redactar un documento en este formato, por ejemplo en GitHub.
Negrita - ?
Itálicas - As typically used in English writing, to add emphasis, or draw attention.
"Doble comillas"
'Simple comillas' son valores literales para ser ingresados u observados
Balas - Acciones que instruyen al usuario a tomar. Como en este listado.
Lista numerada - Sin uso?
Tildes \` Se utiliza para envolver texto, vea el siguiente ejemplo.
Highlighted words (envuelto por tildes) se refiere típicamente a texto o elementos, típicamente literales, en la aplicación, que generalmente son parte de la interfaz de usuario (a diferencia de los datos dinámicos que se muestran). Por ejemplo, pueden estar en nombres de botones o campos como Data, Tasks, Favourite tabs
Citas en linea - ?? (use "> ")
Esta es una cita en linea
Bloque de triple comillas - úselo para ejemplos literales. Ponga tres comillas \`\`\` antes del bloque de texto y 3 comillas al final del mismo. Esto dará como resultado el siguiente bloque de codigo.
`,76),r=[i];function s(l,d){return o(),a("div",null,r)}const u=e(t,[["render",s],["__file","contributing.html.vue"]]),p=JSON.parse('{"path":"/es/develop/contributing.html","title":"Contribuyendo","lang":"es-ES","frontmatter":{"sidebarPosition":30},"headers":[{"level":2,"title":"Ideas, solicitud de caracteristicas","slug":"ideas-solicitud-de-caracteristicas","link":"#ideas-solicitud-de-caracteristicas","children":[{"level":3,"title":"Proveer una interfaz o una idea de flujo de trabajo","slug":"proveer-una-interfaz-o-una-idea-de-flujo-de-trabajo","link":"#proveer-una-interfaz-o-una-idea-de-flujo-de-trabajo","children":[]},{"level":3,"title":"Provea una sugerencia para una funcionalidad o una mejora por medio de un video","slug":"provea-una-sugerencia-para-una-funcionalidad-o-una-mejora-por-medio-de-un-video","link":"#provea-una-sugerencia-para-una-funcionalidad-o-una-mejora-por-medio-de-un-video","children":[]}]},{"level":2,"title":"Codigo","slug":"codigo","link":"#codigo","children":[{"level":3,"title":"Siga las convenciones de codigo de TaxonWorks","slug":"siga-las-convenciones-de-codigo-de-taxonworks","link":"#siga-las-convenciones-de-codigo-de-taxonworks","children":[]},{"level":3,"title":"Submit changes to the code base or repository","slug":"submit-changes-to-the-code-base-or-repository","link":"#submit-changes-to-the-code-base-or-repository","children":[]},{"level":3,"title":"Documentar el codigo?","slug":"documentar-el-codigo","link":"#documentar-el-codigo","children":[]}]},{"level":2,"title":"Documentación","slug":"documentacion","link":"#documentacion","children":[{"level":3,"title":"Editando","slug":"editando","link":"#editando","children":[{"level":4,"title":"En linea","slug":"en-linea","link":"#en-linea","children":[]},{"level":4,"title":"Que rama debería utilizar?","slug":"que-rama-deberia-utilizar","link":"#que-rama-deberia-utilizar","children":[]},{"level":4,"title":"Fuera de linea","slug":"fuera-de-linea","link":"#fuera-de-linea","children":[]}]},{"level":3,"title":"Incluyendo una captura de pantalla","slug":"incluyendo-una-captura-de-pantalla","link":"#incluyendo-una-captura-de-pantalla","children":[{"level":4,"title":"Markdown para imágenes con subtitulo","slug":"markdown-para-imagenes-con-subtitulo","link":"#markdown-para-imagenes-con-subtitulo","children":[]},{"level":4,"title":"HTML para imágenes con subtitulo","slug":"html-para-imagenes-con-subtitulo","link":"#html-para-imagenes-con-subtitulo","children":[]}]},{"level":3,"title":"Agregar un archivo","slug":"agregar-un-archivo","link":"#agregar-un-archivo","children":[]},{"level":3,"title":"Ordenando el contenido del menu lateral","slug":"ordenando-el-contenido-del-menu-lateral","link":"#ordenando-el-contenido-del-menu-lateral","children":[{"level":4,"title":"sidebarPosition","slug":"sidebarposition","link":"#sidebarposition","children":[]},{"level":4,"title":"sidebarParentPosition","slug":"sidebarparentposition","link":"#sidebarparentposition","children":[]},{"level":4,"title":"Orden por nombre de archivo.","slug":"orden-por-nombre-de-archivo","link":"#orden-por-nombre-de-archivo","children":[{"level":5,"title":"Resultado del menu lateral:","slug":"resultado-del-menu-lateral","link":"#resultado-del-menu-lateral","children":[]}]},{"level":4,"title":"Ordenar por medio de la variable sidebarPosition","slug":"ordenar-por-medio-de-la-variable-sidebarposition","link":"#ordenar-por-medio-de-la-variable-sidebarposition","children":[{"level":5,"title":"Resultado del menu lateral:","slug":"resultado-del-menu-lateral-1","link":"#resultado-del-menu-lateral-1","children":[]}]}]},{"level":3,"title":"Convenciones de estilo","slug":"convenciones-de-estilo","link":"#convenciones-de-estilo","children":[]}]},{"level":2,"title":"Gestión de proyecto","slug":"gestion-de-proyecto","link":"#gestion-de-proyecto","children":[{"level":3,"title":"Categorizar un issue en GitHub","slug":"categorizar-un-issue-en-github","link":"#categorizar-un-issue-en-github","children":[]}]}],"git":{"updatedTime":1716075775000,"contributors":[{"name":"jlpereira","email":"pepelui@outlook.com","commits":2},{"name":"Tom Klein","email":"twointofive@gmail.com","commits":1}]},"filePathRelative":"es/develop/contributing.md"}');export{u as comp,p as data};
diff --git a/assets/contributing.html-fneavcB-.js b/assets/contributing.html-fneavcB-.js
new file mode 100644
index 00000000..8e2f43ec
--- /dev/null
+++ b/assets/contributing.html-fneavcB-.js
@@ -0,0 +1,33 @@
+import{_ as e,c as t,o as a,b as o}from"./app-Bwgh_xIT.js";const i={},n=o(`
First, thanks, this is complicated stuff. Interface (e.g. forms, reports, searches) mockups are graphical ways of asking for new features. We love to see them. To create a mock-up you can use tools like Illustrator, Photoshop, or more technical design tools like Balsamiq or Sketch, or just draw them on paper and take a picture with your phone. The issue templates have inputs for handling images, just drag and drop them there. Add a little story, or multiple pictures to help describe how you might use the interface.
Send! It is super useful for you to record your screen, or position a video camera to capture your work on-screen and arround you. This way we see exactly how you work. You can send us big videos through file sharing services like http://www.dropsend.com/. Find ways to Contact us here.
This software and workflow together make it possible for all to contribute to TaxonWorks Doc. Note all the pages here in docs.taxonworks.org have an "edit this page" feature. Scroll down to bottom of this page to see it.
Add a (very) brief description of your change in the filed that has Update README.md in muted colors
Add a longer optional description in the bigger box, if you want
In your message not to use words like "Changed, tweaked, updated", describe what was done
Choose the second option Create a new branch .... There is an exception to this, if your changes are small, and ready to go directly to the public site, then you can commit to the development branch.
Click Commit changes again
A TaxonWorks Docs GitHub repository team member will review, make edits, ping you with questions if needed, and then ultimately accept the pull request to "merge" this our documentation.
In deciding which branch to make a change on start by asking the question: "Is my change ready to go live, right now?" If the answer is yes (and you have permissions) then you can commit to the development branch. If the answer is no (e.g. you want to further refine your text), then you should commit to a new branch.
In addition:
The development branch is the staging ground for the main branch.
You should always assume that that development branch changes will go live at any time.
Development changes may accumulate before moving to main.
The main branch must never be committed to directly. Changes to main happen when development is merged into it.
It is always safest, and OK, to start a new branch.
It's best to limit the scope of your changes on each new branch.
If you have large/ongoing changes to your branch its useful to start your editing session by merging development into your branch. This keeps the differences between development and your branch minimal.
If you are editing locally, make sure you syncronize your changes with those on the remote server (git pull) before you start your editing session.
In adding documentation, you will note that on any page at docs.taxonworks.org you can click the Edit pencil icon to add / edit text. To manage the screenshot image files we add to the documentation, we use TaxonWorks Meta Project hosted on sfg.taxonworks.org. To add screenshots to this documentation, you'll need to become a member of that TaxonWorks Meta Project. Let us know you want to be added (e.g. send dlpaul AT illinois DOT edu an email, or ping us on gitter or our TaxonWorks Slack Workspace). When taking screenshots, note the resolution of your computer's monitor makes a difference if these images are sharp and clear or out of focus.
Take the desired screenshots.
Upload these images (in bulk or one-at-a-time) to the TaxonWorks Meta Project using the New Image task.
In TaxonWorks, find the generated image link URLs, using the Filter Image task. Try Filter Image using the Housekeeping filter to limit your result set to only images uploaded by you.
In the resulting set, click on the desired image, then
Click the Navigate radial under the image and select Show.
From Attributes copy the short URL to orginal URL link.
Return to editing documentation and use the Markdown format or HTML format below to insert image URLs (examples next).
Note that both methods allow you to specify the image size.
Examples here show the markdown (md) format for adding a caption to an image.
Select one of the four options below for your caption. Put that text string into the documentation as described next.
With the position option, choose left, center, or right which aligns your caption text according to what you pick.
Enter the text of your choice in-between the brackets [caption text goes here].
Paste in the short URL to orginal URL link (from Filter Image > Navigate radial > Show > Attributes).
Add alt text in-between brackets. It is best practice to include this for accessibility.
(Optional) Declare the width or height or both of the image to control the size displayed.
The default sizes works well. Sometimes, depending on the screenshot, it might appear too large and then this option gives you the ability to modify the size.
#position[caption text goes here](link [alt text if you want it])
+#position[caption text goes here](link [alt text if you want it] w{60%})
+#position[caption text goes here](link [alt text if you want it] h{50%})
+#position[caption text goes here](link [alt text if you want it] w{80%} h{50%})
+
Where: In any (README.md or other) documentation file. When: You want to position the content of that document within the context of the other files within that directory.
Where: Only in a README.md. When: You want to position the name of the directory within the context of other directories and files at the level of that directory.
sidebarPosition allows you to change the order of the sidebar regardless of the alphabetical order of the files. Let's take the example above, but now we're going to add sidebarPosition in each file to change the order:
Filename: foo.md
---
+sidebarPosition: 200
+---
+# A is the first letter of this title
+
Filename: bar.md
---
+sidebarPosition: 100
+---
+# B is the first letter of this title
+
We use Markdown. Many guides exist, for example on GitHub.
Bold - ?
Italics - As typically used in English writing, to add emphasis, or draw attention.
"Double quotes" - follow typical English use.
'Single quoted words' are literal values to be input or observed
Bullets - Actions we are instructing the user to take. Do this now.
Numbered bullets - Unused?
Backticks \` are used to wrap text. See next.
Highlighted words (surrounded by backticks) refer to, typically literal, text or elements in the application, that are generally part of the user interface (as opposed to dynamic data being displayed). For example they might be on button or field names like "Notice the Data, Tasks, Favourite tabs".
Inline quotes - ?? (use "> ")
this is an inline quote
Triple-tick blocks - use these for literal examples. Put 3 backtick marks \`\`\` before the text block and 3 backtick marks after the text. This results in the following block in documentation.
`,76),s=[n];function r(l,d){return a(),t("div",null,s)}const h=e(i,[["render",r],["__file","contributing.html.vue"]]),u=JSON.parse('{"path":"/develop/contributing.html","title":"Contributing","lang":"en-US","frontmatter":{"sidebarPosition":30},"headers":[{"level":2,"title":"Ideas, feature requests","slug":"ideas-feature-requests","link":"#ideas-feature-requests","children":[{"level":3,"title":"Provide an interface or workflow idea","slug":"provide-an-interface-or-workflow-idea","link":"#provide-an-interface-or-workflow-idea","children":[]},{"level":3,"title":"Provide a suggestion for a feature or improvement via a video","slug":"provide-a-suggestion-for-a-feature-or-improvement-via-a-video","link":"#provide-a-suggestion-for-a-feature-or-improvement-via-a-video","children":[]}]},{"level":2,"title":"Code","slug":"code","link":"#code","children":[{"level":3,"title":"Follow TaxonWorks code conventions","slug":"follow-taxonworks-code-conventions","link":"#follow-taxonworks-code-conventions","children":[]},{"level":3,"title":"Submit changes to the code base or repository","slug":"submit-changes-to-the-code-base-or-repository","link":"#submit-changes-to-the-code-base-or-repository","children":[]},{"level":3,"title":"Document the code?","slug":"document-the-code","link":"#document-the-code","children":[]}]},{"level":2,"title":"Documentation","slug":"documentation","link":"#documentation","children":[{"level":3,"title":"Editing","slug":"editing","link":"#editing","children":[{"level":4,"title":"Online","slug":"online","link":"#online","children":[]},{"level":4,"title":"What branch should I use?","slug":"what-branch-should-i-use","link":"#what-branch-should-i-use","children":[]},{"level":4,"title":"Offline","slug":"offline","link":"#offline","children":[]}]},{"level":3,"title":"Including screenshots or images","slug":"including-screenshots-or-images","link":"#including-screenshots-or-images","children":[{"level":4,"title":"Image caption markdown (writing docs)","slug":"image-caption-markdown-writing-docs","link":"#image-caption-markdown-writing-docs","children":[]},{"level":4,"title":"HTML for image with caption","slug":"html-for-image-with-caption","link":"#html-for-image-with-caption","children":[]}]},{"level":3,"title":"Adding a file","slug":"adding-a-file","link":"#adding-a-file","children":[]},{"level":3,"title":"Ordering sidebar content","slug":"ordering-sidebar-content","link":"#ordering-sidebar-content","children":[{"level":4,"title":"sidebarPosition","slug":"sidebarposition","link":"#sidebarposition","children":[]},{"level":4,"title":"sidebarParentPosition","slug":"sidebarparentposition","link":"#sidebarparentposition","children":[]},{"level":4,"title":"Order by filename","slug":"order-by-filename","link":"#order-by-filename","children":[{"level":5,"title":"Sidebar result:","slug":"sidebar-result","link":"#sidebar-result","children":[]}]},{"level":4,"title":"Order by sidebarPosition variable","slug":"order-by-sidebarposition-variable","link":"#order-by-sidebarposition-variable","children":[{"level":5,"title":"Sidebar result:","slug":"sidebar-result-1","link":"#sidebar-result-1","children":[]}]}]},{"level":3,"title":"Style conventions","slug":"style-conventions","link":"#style-conventions","children":[]}]},{"level":2,"title":"Project management","slug":"project-management","link":"#project-management","children":[{"level":3,"title":"Categorize an Issue on Github","slug":"categorize-an-issue-on-github","link":"#categorize-an-issue-on-github","children":[]}]}],"git":{"updatedTime":1716075775000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":12},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":6},{"name":"Tom Klein","email":"twointofive@gmail.com","commits":1},{"name":"jlpereira","email":"pepelui@outlook.com","commits":1}]},"filePathRelative":"develop/contributing.md"}');export{h as comp,u as data};
diff --git a/assets/conventions.html-zLGNohUl.js b/assets/conventions.html-zLGNohUl.js
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+import{_ as e,c as t,o,b as a}from"./app-Bwgh_xIT.js";const i={},n=a('
TaxonWorks offers conventions via a unique user interface building in forward-aware methods like automated data validation to aid navigation and data fitness.
TW seeks to offer a user interface (UI) that is as intuitive as possible that supports elegant software features to improve both the experience and the data products.
This guide and manual exemplify one way in which the Species File Group and TaxonWorks endeavor to build a sustainable, open, transparent community. The software and process for building and maintaining the content here were selected specifically for ease of community curation of this resource.
The structure, tasks, and features of TW focus on addressing specifically-stated needs of those using the product. We use an agile, "epic story" approach that can be summarized as: As a [your role], I want to do [your task], in order to accomplish [some product].
Note color conventions used in the TW UI offer information to orient the observer to more information (e.g. this task is still under development, or these data are shared across projects).
This screenshot provides a quick overview of the TW User Interface after log in. In the caption, you will find brief descriptions of each highlighted feature. If you have an account, please log in and click to try header menu options.
Legend: The TaxonWorks User Interface after signin. See items explained next
In the header menu (left-to-right), click
TaxonWorks to return to this Dashboard view
(copy) software version number (e.g. v0.28.0)
Issues to submit an idea or issue to GitHub
Project to manage a specific project
Administration to see/access all projects you administer
Account to access your own account information
Sign out/in
In the main section (left-to-right): click items under the headers. Options under Projects give you access to all your projects. With Data you can view recently created data added for that project. With Preferences you can order the User Interface hub options Tasks, Data, and Favorites.
On the far bottom right, note the four icons (top to bottom).
Click a half-circle icon on the right side to open a panel
The red circle opens the PDF Document viewer. The green circle gives you a Pinboard to access frequently used items like source PDFs. With the blue circle, you get a Clipboard for frequently used text. The orange circle provides built-in context-dependent Help.
Next, for any given Project you select, notice the UI changes once you click Administration for that Project. In the Administration module you can, for example: see/add project members, and control permissions. In any TW sandbox, you can add yourself to other projects using the Administration link. See next for more about the Administraion tools.
Legend: The TaxonWorks Project Administration UI. See options explained next.
In the main section under Projects you can click to create a New Project or use Projects overview to find a Project and add a current TW user as a member.
From the Users section, you have options to add a New user, add multiple users using Batch add new, List all users, and see the Activity for all Projects and Users.
Under the Data topic, using Overview you can create specific reports for different data types and projects. With Health you find any data issues that the TW software has detected. Reindex opens an option for you to create Darwin Core (standard) occurrence records.
Generate new token if you want to be able to access your data programatically
clear api access token if you need / want to stop all public programatic access to your data.
Click Create Project.
As a result, your Dashboard list will include the new Project. If for some reason you find you need to edit the name of your project, it's also editable after creation.
Users need to be added to TW before they can become Project members. Once a user, they can be added as members, to any project desired. If you are flagged as an administrator you can do everything in the workbench. As an admin, you see the Adminstration link in the header menu. Feel free to add users to your sandbox through the Administration link. If you do, please provide them a link to this Terms of Use Page and our Collaboration Understanding.
Sandbox Only: Feel free to add yourself to projects that are currently not visible to you. Steps to do this:
Click Administration (top right)
Click Projects overview (on left)
Click List
Review the list, select one using Double click for that row
Before adding anyone to the list of TW Users, please check the list as someone may already be in the TW Community through another project. In this case, you'll need to add them to your project as a new member. If they do need a User account, see the following steps.
Signin to TaxonWorks
Select the Project of interest
Click Administration in the header menu
Then under Users, click list to search existing list.
If you do not find the name / email you are looking for, go back one step to Users and click New and fill out the form.
Type their Name
Enter their Email
Provide a Password (It will be temporary, they will need to reset it).
Retype the Password
(Optional) select Is administrator if you want them to have this role.
(Optional) select the matching Person if they are in TaxonWorks.
(Optional) select Generate new api access token if desired for a User that wants to query the TW Project database programmatically.
Send the new User (and soon-to-be Project member) an email with instructions to read the Terms of Use Page and our Collaboration Understanding. They will also need to reset password.
Note: you can also go to Batch add new to add many users at one time (see under Administration > Users > Batch add new) and you will need their email and name string for each new user.
Note: in TaxonWorks a Person differs from a User. To be a Person in TaxonWorks, you have been vetted and with best practice, you have a globally unique identifier (e.g. an ORCiD or Wikidata Q number).
When you want to add an existing TW User to a Projectsee these steps:
After signin, select the desired Project
Then click Project in the header menu
Under Members click Add project member
Search the User and once found, click to select
(Optional) select Is administrator if desired
Click Create Project member
(Optional) you may want to send the new Project members an email if need be with a link to the new project.
If you need to add many folks at one time, use the Add many project members option instead. (See Project > Members > Add many project members) and select the desired individuals and click Create project members.
Note that once you log into a given project, you see 3 options for interacting with others and data. See the Tasks, Data, and Favorites tabs.
The Tasks provide you with one-click access to working on a specific activity such as Filter Sources for the ones you seek or Comprehensive Digitization of specimen data.
currently 80 tasks exist in TW
tasks can be customized
new tasks can be written
you can search tasks
tasks are associated with given global concepts (e.g. Nomenclature, Source, Biology, Collection object, Collecting event, Image, Matrix, dna, etc.)
With the Favorites tab, you can store your most-used tasks (aka activities) for quick access to what you do most often.
To add a task to appear in your Favorites tab, click the 'star' on the task card.
The Data tab provides you with more of a traditional table view of information as stored in TW. Here you begin to get a sense of how the data are structured and related in TW.
If you would like more details about the TW Data Model, see the Data section of docs.taxonworks.org
Some icons in TaxonWorks help you move around (i.e. "navigate") in the software. Other icons touch the database, providing you with functions to add data or delete something. In TaxonWorks, icon button colors convey this idea.
Green buttons = write to the database
Red buttons = delete from the database
Blue buttons = activate something in the interface
Note also, all icons with a blue circle and white middle are Radials and serve to help you add information to (i. e. to annotate) the object you are looking at (e. g. the Source publication record, the CollectionObject record, the Collecting Event record, the TaxonName record, etc). In other words, a tool found many places in TW, that integrates commonly used functions or tasks for annotating things (adding related information) in one place. The particular functions found after click are context dependent.
Icon
Icon Name
Purpose of Icon
Radial Icons in TaxonWorks
use these to add information to the current object of interest, move to a different area in TW, or select objects of interest. The particular functions found after click show you what types of information you can add or actions you can take.
Annotate Radial
use this to add information to the current object of interest. The particular functions found after click are show you what types of information you can add.
Navigate Radial
use this icon to move across to different areas in TaxonWorks
Mass Annotate Radial
use this icon to add information to many records at once in TaxonWorks
Filter Radial
use this icon to select a set of records from a search in TaxonWorks using the Filter task (e. g. Filter Nomenclature, Filter Sources, Filter Collection Objects, etc.)
Quick Forms Radial
use this to bring up commonly used forms associated with OTUs, such as Asserted distributions or Biological Associations
Label Radial
use this to create labels
Linker Radial
use this to send selected results from a filtered search to another Task in TaxonWorks to further refine your data subset
Loan Radial
select objects to loan or that are being returned
Browse Taxa
moves you from a taxon name to its associated OTU
Browse Nomenclature
takes you from an OTU to its associated taxonomic name
Pinboard
Add (if green) or Remove (if red) an item from your Pinboard. If the icon is blue, the item has been selected as the default in your pinboard and you can add it to a field automatically, for example, with literature citations.
Edit
With this icon, you may edit a given item. For example, from the Browse nomenclature page, this icon takes you to the Edit taxon name page associated with the taxon.
Trashcan
Use this to remove the current record from the database
As of this writing, you can only be logged into one instance (one project) of TW at-a-time.
You can write your own tasks in TW? Ask us how.
',52),s=[n];function r(d,c){return o(),t("div",null,s)}const h=e(i,[["render",r],["__file","conventions.html.vue"]]),u=JSON.parse('{"path":"/guide/Manual/conventions.html","title":"The User Interface","lang":"en-US","frontmatter":{"sidebarPosition":20},"headers":[{"level":2,"title":"Philosophy","slug":"philosophy","link":"#philosophy","children":[]},{"level":2,"title":"Logging in","slug":"logging-in","link":"#logging-in","children":[]},{"level":2,"title":"Administration","slug":"administration","link":"#administration","children":[{"level":3,"title":"Add New Project","slug":"add-new-project","link":"#add-new-project","children":[]},{"level":3,"title":"Adding folks to projects","slug":"adding-folks-to-projects","link":"#adding-folks-to-projects","children":[]},{"level":3,"title":"Add New User","slug":"add-new-user","link":"#add-new-user","children":[]},{"level":3,"title":"Add Project Member","slug":"add-project-member","link":"#add-project-member","children":[]},{"level":3,"title":"Inside a Project","slug":"inside-a-project","link":"#inside-a-project","children":[]}]},{"level":2,"title":"Explore TW Tasks","slug":"explore-tw-tasks","link":"#explore-tw-tasks","children":[]},{"level":2,"title":"Icons in TaxonWorks","slug":"icons-in-taxonworks","link":"#icons-in-taxonworks","children":[]},{"level":2,"title":"Did you know","slug":"did-you-know","link":"#did-you-know","children":[]}],"git":{"updatedTime":1686866578000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":17},{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":2},{"name":"mjy","email":"diapriid@gmail.com","commits":2}]},"filePathRelative":"guide/Manual/conventions.md"}');export{h as comp,u as data};
diff --git a/assets/customization.html-BPiCMdGT.js b/assets/customization.html-BPiCMdGT.js
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+import{_ as o,c as e,o as a,a as t}from"./app-Bwgh_xIT.js";const l={},n=t("h1",{id:"customization",tabindex:"-1"},[t("a",{class:"header-anchor",href:"#customization"},[t("span",null,"Customization")])],-1),i=t("p",null,"TODO",-1),s=t("h2",{id:"controlled-vocabulary-terms",tabindex:"-1"},[t("a",{class:"header-anchor",href:"#controlled-vocabulary-terms"},[t("span",null,"Controlled Vocabulary Terms")])],-1),c=t("p",null,"TODO",-1),r=[n,i,s,c];function d(m,u){return a(),e("div",null,r)}const h=o(l,[["render",d],["__file","customization.html.vue"]]),p=JSON.parse('{"path":"/guide/Manual/customization.html","title":"Customization","lang":"en-US","frontmatter":{"sidebarPosition":330},"headers":[{"level":2,"title":"Controlled Vocabulary Terms","slug":"controlled-vocabulary-terms","link":"#controlled-vocabulary-terms","children":[]}],"git":{"updatedTime":1712178034000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"guide/Manual/customization.md"}');export{h as comp,p as data};
diff --git a/assets/data-quality.html-DbfyvRgN.js b/assets/data-quality.html-DbfyvRgN.js
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+import{_ as e,c as t,o as a,b as o}from"./app-Bwgh_xIT.js";const i={},n=o('
The nature of data, particularly aspects of quality (e.g. completeness, consistency, compliance) are directly related to whether or not it can be re-used (the R in FAIR). Quality is an abstract and rather subjective term, one difficult to pin down. Fidelity* may prove more a more tractable term. Conceptual and implemented means to improve data quality in and around TaxonWorks.
This documentation originated via the co-organization of a workshop at Digital Data 8, Data cleaning for maximum impact: Tools and workflows for data providers to efficiently find and fix data quality issues. Other co-organizers produced similar documentation resulting in a cross-platform page can be found at iDigBio: Data Quality Toolkit 2024. Each section below is linked to its corresponding topic on that iDigBio page.
Our TW philosopy on data quality or fidelity is multifaceted and can be thought of as the concepts of prevention, discovery, and resolution as applied to a spectrum of processes, from designing the data-models, to implementing validations, to creating tools and workflows facilitating discovery and visualization, to building user-interfaces that curators use to resolve issues, to reflecting feedback from external sources back into the system.
Many of the issues highlighted below can be prevented at inception (when data are captured). At a low level this can happen during data-model design and implementation. For example in TaxonWorks we:
Carefully model our domain (models) so that there is a solid basis for expanding the semantics of what we are capturing. This helps to prevent the addition of fields that seem useful at the time but that ultimately confuse our understanding of the data as the system evolves.
Isolating data fields from fields that facilitate TaxonWorks functionality. This separation of concerns ensures we can efficiently implement globally-relevant data-cleaning (e.g. stripping bad characters) and iterative checks on the data while not being confused by fields that don't require such.
Only permit data changes through a single API (TaxonWorks models), as opposed to updates directly to the database. This forces all validations to be checked when data enters the system, greatly improving data integrity.
Choosing either the database or the data-model as the location of data validation functions (not both, TaxonWorks validates in the model)
Creating (sometimes complex) tests that check that the validations implemented still hold, these are run on every single commit to the repository.
Using a convention to implement our data models and their relationships to one another (e.g. Rails ActiveRecord models)
In general, when, where, and how you find any data anomalies will vary, not only with respect to TaxonWorks but in working with data in general. For example, you might become aware of issues when:
Mapping you data to an external standard, perhaps during migration to another database or share with an aggregator
Cleaning data up in a spreadsheet before upload to a workbench like TaxonWorks
Exploring your exported data with tools like OpenRefine, or via R, or via another API
Receiving feedback from another source (e. g. GBIF or iDigBio or ALA or OBIS or Bionomia)
Hearing from someone on the internet sees something and contacts you
Perusing data already in your own database
Visualizing issues in day-to-day work, for example via the hundreds of notices possible in TaxonWorks on its "soft validation" framework.
Using your database data visualization tools to see distinct values in a given field (e. g. Project vocabulary task in TaxonWorks) or on a map.
Example means to resolve the data are detailed in the specifics below. In addition to those one of the important ways to resolve problems is to use TaxonWorks models in scripts to batch process and fix data.
To extend the value and scope of this work we link to the work of the Biodiversity Information Standards (TDWG) Biodiversity Data Quality Task Group (BDQ). We list the BDQ tests relevant to each issue, where they exist. With these connections, we hope to enhance the software developer's vision and work to connect to the BDQ tests to the workbench functionality around preventing, finding, and fixing these types of issues.
We gratefully acknowledge the efforts of this TDWG Task Group and the contributions and conversations with Paul Morris and Lee Belbin in figuring out how to do this. Special thanks to Paul Morris for work done to map the BDQ tests to the specific data quality issues highlighted in this workshop and on this page.
Issues below are grouped into the: Identifiers (e .g. catalog numbers), Time (e. g. dates), Place (aka geography, location), Taxon, and Other and Tools and Resources.
WARNING
TaxonWorks only references many DarwinCore fields on export of the data, i.e. in the translation of its data model to an external format.
Duplicate Identifiers are prevented in the data model. This prevents errors in initial or subsequent (bulk OR one-by-one) uploads to TW. We use Namespaces and a simple Identifier ontology to ensure sets of Identifiers whose members are all unique.
catalogNumber is only invoked as a column when exporting to Darwin Core format (it's not a specific field in a TaxonWorks model). When multiple objects are identified by the same catalogNumber we associate the corresponding Identifier to a virtual container. This lets us export a "duplicate" catalogNumber in the export for each occurrence record (which is uniquely identified by a UUID) while maintain specific data on individual specimens. catalogNumbers that appear identical in their rendering can be differentiated via different Namespaces if it can be determined that they were created via independent processes. Finally, you can extend any DarwinCore export with a custom data-attribute that might reference, say dwc:otherCatalogNumbers.
In TaxonWorks, different types of records have dates associated, for example: the event date for a given Collecting Event, or the date identified (that is, date determined), or the date georeferenced. Dates out-of-expected bounds would include several kinds of impossible dates. That is, dates in the future or dates before the objects were actually ever collected or dates that are not possible with the birth and death dates for the person who collected/identified/observed/georeferenced/imaged the object/s. These could be grouped as
Find outlier dates using the Filter Collecting Event task, the Filter Collection Object task, and you can use the Project Vocabulary task to peak inside each field in your database to see distinct values and the records with those values.
Using the date range method to find outlier dates with the Filter Collecting Event task
Navigate to the Filter Collecting Event task
Scroll down to the Collecting Event filter section
Enter date range to search
e. g. to check for future out-of-bounds dates try putting "tomorrow's" date in for the start date and some date way into the future for the End date
Click Filter to see resulting records.
TIP
Note you can click any column to sort on that column (which sorts only for the records showing on that page). This makes it simpler to see outliers in a date-related column. These sets can also be downloaded as CSV files if need be.
Find outlier dates using the Project Vocabulary task. With this task, one can see the unique values present for a given field and how many times that string/value occurs. You click on one of the results of the output and see the associated records having that value. For the out-of-expected-bounds-date use case, one could see odd unexpected dates easily.
Find outlier dates based on someone's lifespan, when known. In the future, you can expect that if you have the active years for a given person entered into the database, and that person is linked to a record where the date collected or identified is not within their active years, you will be able to find these records.
Fix the outlier dates found from the above Filter Collecting Event task search.
In the result set, you can navigate to a single record and edit that one
You can use the download csv version of the results if you have a lot of records and want to sort by year in a spreadsheet to see the extent of the year bounds.
You can sort by year by clicking on a given column, however, it is only sorting the records on that page (note the number of records per/page can be increased).
If using the DwC Occurrence Importer and you provide the eventDate (in YYYY-MM-DD format) and you provide the dwc:day, dwc:month, and dwc:year, the importer software checks for consistency.
If using the DwC Occurrence Importer and you provide the eventDate (in YYYY-MM-DD format) only, we derive the dwc:day, dwc:month, and dwc:year on import.
After upload, the year, month, and day fields can be edited, there is no single eventDate field which prevents these from potentially getting out of sync.
If you provide coordinates on upload, we compute the geographic units based on the gazetteer information. So we don't have this issue specifically. You can potentially see outliers using the following method.
Find and Fix
Go to Filter collecting events
Search for the area of interest, (e. g. United States and pick Descendants)
Click Filter
In the resulting set, in the left sidebar, click the linker icon to get the Radial linker
Select Spatial Summary which gives you a scatter plot where the x-axis is longitude, the y-axis is latitude
If there are longitudes with positive (or other outlier non-expected) values, you will be able to see them and go to those records to debug.
TIP
Using the Collecting Event software, if you provide spatial constraint (choose a GeographicArea with shape) and try and provide a point outside that, you are not allowed to. We note at the same time, you can put whatever conflicting info you want in verbatim_ fields, these are not validated.
Coordinates are exported as Geo referenced, i.e. they can not be illegal values. They can of course be based on points placed in error. Errors are minimized due to cross-referencing to geo-spatial gazetteers ensuring that the points dropped are within 10km of the place selected.
Selecting any GeographicArea happens in one place in TaxonWorks, so you automatically get spatial and parent validation going up.* In other words, if you provide the lower geography, we derive the higher geography where there is information in our gazetteers to do so.
If a country is reported and we have access to a corresponding ISO code (true for a majority of cases), then they are always matched, i.e. they are derived from a unified source, not manually entered independently.
TaxonWorks makes use of an internally managed GeographicArea gazeteer. Selecting a finer resolution entity (e.g. county, state) permits us to crawl the parenthood to fill in the pertinent data.
WARNING
TaxonWorks also does spatial lookup for Georeference point data. The lookup algorithm can error based on limits to the resolution of the referenced gazeteers. In this case one cap prioritize the use of GeographicArea to over-ride the spatial lookup.
Missing data here are the norm for historical data. For de-novo capture TaxonWorks exports a number of types as estimated from the processes by which the Georeference was captured or an explicity Protocol reference.
A huge variety of nomenclatural nuances can be specifically classified and identified in TaxonWorks, synonymous and misspelled names included. All of these represent the historical record. TaxonDeterminations are linked to these names and a CollectionObject as a bridging step. Presenting synomous or misspelled names during export is not only possible but required in various cases (for example for nomenclatural catalogs).
Unknown higher taxonomy is highly specific to the purpose of use of the data. There is no one true classification of nomenclature, or taxa. Syncronizing of TaxonWorks data to external taxonomies is best done via the processes that merge or take TaxonWorks data into a new system.
All data are encoded as UTF-8. TaxonWorks pre-processes all strings before writing (persisting) them to remove a handful of well-known issues with encoding, for example trimming white-space and removing various invisible characters.
We generate dwc:basisOfRecord, so a non-issue for TW. If an issue on Import, our Importer software will tell you. With the Importer you can "find" and "replace" any non-standard value and then continue the upload.
GBIF’s data quality flags NOTE: in TaxonWorks, we pull GBIF DQ data back for you into the user-interface so you can evaluate the feedback without leaving TaxonWorks.
OBIS Manual (e. g. their Data Laundry help and community) See also Gan Y-M, Perez Perez R, Provoost P, Benson A, Peralta Brichtova AC, Lawrence E, Nicholls J, Konjarla J, Sarafidou G, Saeedi H, Lear D, Penzlin A, Wambiji N, Appeltans W (2023) Promoting High-Quality Data in OBIS: Insights from the OBIS Data Quality Assessment and Enhancement Project Team . Biodiversity Information Science and Standards 7: e112018. https://doi.org/10.3897/biss.7.112018
Linter tools offer another way to evaluate and tidy up your data. For example, you have a BibTeX file (from EndNote, Zotero, or elsewhere) that seems to have errors. You can use online tools that help you find and fix formatting (syntax) errors.
Fidelity - as referenced by Erica Krimmel at TaxonWorks Together 2024 as a term that may more exactly convey what we can manage when we talk about making our data as fit-for-purposes (known and imagined) as possible (rather than the more subjective term of quality).
',117),r=[n];function s(l,d){return a(),t("div",null,r)}const h=e(i,[["render",s],["__file","data-quality.html.vue"]]),p=JSON.parse('{"path":"/guide/data-quality.html","title":"Data Quality Help and Hints","lang":"en-US","frontmatter":{"sidebarPosition":55},"headers":[{"level":2,"title":"Motivation","slug":"motivation","link":"#motivation","children":[]},{"level":2,"title":"Rationale and 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Date","slug":"filter-collecting-event-by-date","link":"#filter-collecting-event-by-date","children":[]}]},{"level":3,"title":"eventDate and year month day","slug":"eventdate-and-year-month-day","link":"#eventdate-and-year-month-day","children":[]}]},{"level":2,"title":"Place","slug":"place","link":"#place","children":[{"level":3,"title":"Coordinates Zero","slug":"coordinates-zero","link":"#coordinates-zero","children":[]},{"level":3,"title":"Coordinates Do Not Fall Within Named Geographic Unit","slug":"coordinates-do-not-fall-within-named-geographic-unit","link":"#coordinates-do-not-fall-within-named-geographic-unit","children":[]},{"level":3,"title":"Georeference Metadata with no Associated Georeference","slug":"georeference-metadata-with-no-associated-georeference","link":"#georeference-metadata-with-no-associated-georeference","children":[]},{"level":3,"title":"Elevation Unlikely","slug":"elevation-unlikely","link":"#elevation-unlikely","children":[]},{"level":3,"title":"Improperly Negated Latitudes Longitudes","slug":"improperly-negated-latitudes-longitudes","link":"#improperly-negated-latitudes-longitudes","children":[]},{"level":3,"title":"Invalid Coordinates","slug":"invalid-coordinates","link":"#invalid-coordinates","children":[]},{"level":3,"title":"Lower Geography Values Provided, but No Higher Geography","slug":"lower-geography-values-provided-but-no-higher-geography","link":"#lower-geography-values-provided-but-no-higher-geography","children":[]},{"level":3,"title":"Minimum and Maximum Elevation Values Mismatched","slug":"minimum-and-maximum-elevation-values-mismatched","link":"#minimum-and-maximum-elevation-values-mismatched","children":[]},{"level":3,"title":"Mismatched Country and CountryCode Values","slug":"mismatched-country-and-countrycode-values","link":"#mismatched-country-and-countrycode-values","children":[]},{"level":3,"title":"Mismatched Geographic Terms","slug":"mismatched-geographic-terms","link":"#mismatched-geographic-terms","children":[]},{"level":3,"title":"Missing Geodetic Datum","slug":"missing-geodetic-datum","link":"#missing-geodetic-datum","children":[]},{"level":3,"title":"Missing Latitudes Longitudes","slug":"missing-latitudes-longitudes","link":"#missing-latitudes-longitudes","children":[]},{"level":3,"title":"Misspelled Geographic Unit Names","slug":"misspelled-geographic-unit-names","link":"#misspelled-geographic-unit-names","children":[]}]},{"level":2,"title":"Taxon","slug":"taxon","link":"#taxon","children":[{"level":3,"title":"Misspelled or Invalid Taxonomic Names","slug":"misspelled-or-invalid-taxonomic-names","link":"#misspelled-or-invalid-taxonomic-names","children":[]},{"level":3,"title":"Unknown Higher Taxonomy","slug":"unknown-higher-taxonomy","link":"#unknown-higher-taxonomy","children":[]}]},{"level":2,"title":"Other","slug":"other","link":"#other","children":[{"level":3,"title":"Incorrect Character Encodings","slug":"incorrect-character-encodings","link":"#incorrect-character-encodings","children":[]},{"level":3,"title":"Incorrect Line Endings","slug":"incorrect-line-endings","link":"#incorrect-line-endings","children":[]},{"level":3,"title":"Invalid Individual Count","slug":"invalid-individual-count","link":"#invalid-individual-count","children":[]},{"level":3,"title":"Nonstandardized basisOfRecord Values","slug":"nonstandardized-basisofrecord-values","link":"#nonstandardized-basisofrecord-values","children":[]}]},{"level":2,"title":"External Tools and Resources","slug":"external-tools-and-resources","link":"#external-tools-and-resources","children":[{"level":3,"title":"Footnotes","slug":"footnotes","link":"#footnotes","children":[]}]}],"git":{"updatedTime":1717095660000,"contributors":[{"name":"Deborah Paul","email":"dlpaul@illinois.edu","commits":5},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":1},{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"guide/data-quality.md"}');export{h as comp,p as data};
diff --git a/assets/digitization.html-DUdm7cWf.js b/assets/digitization.html-DUdm7cWf.js
new file mode 100644
index 00000000..9d24ff9b
--- /dev/null
+++ b/assets/digitization.html-DUdm7cWf.js
@@ -0,0 +1 @@
+import{_ as a,r as n,c as o,a as e,d as i,e as s,w as l,b as r,o as d}from"./app-Bwgh_xIT.js";const c={},h=e("h1",{id:"digitization",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#digitization"},[e("span",null,"Digitization")])],-1),u=e("p",null,[e("em",null,"TaxonWorks offers taxonomists, collections staff, and others to collaboratively manage collections data for specimens and related objects.")],-1),p=e("p",null,'Uniquely in TaxonWorks, we make it easy up-front to add customized fields (aka "data attributes") where needed. In addtion, in TW you can upload data mapped to Darwin Core, to specific fields in TW, and to these customized data attributes you add.',-1),g=e("h2",{id:"digitization-quick-start",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#digitization-quick-start"},[e("span",null,"Digitization Quick Start")])],-1),m=r('
To get a sense of what can be tracked regarding specimens in your collection, see the Comprehensive Digitization Task in TW outlined next. Note also that you may enter data into TW record-by-record, or in batch mode (see Import and Export).
[INSERT screenshot of Comprehensive Digitization Task screen here]
There are many places where you can print labels from different tasks in TaxonWorks, including unit trays, specimen labels, and identifiers. The main task where you manage what is finally printed is Print Labels, but labels are generated within a variety of other tasks.
You can generate many labels from many different places, then select which ones to print later?
',14);function f(b,k){const t=n("RouteLink");return d(),o("div",null,[h,u,p,g,e("p",null,[i("TW provides a suite of common tasks help you to manage your digitization and related data. This section assumes you have some familiarity with the "),s(t,{to:"/guide/Manual/conventions.html"},{default:l(()=>[i("TW user interface conventions")]),_:1}),i(" and introduces new user interface features where needed. Next, please familiarize yourself some of the tasks TW offers directly relevant to digitization.")]),m])}const T=a(c,[["render",f],["__file","digitization.html.vue"]]),v=JSON.parse('{"path":"/guide/Manual/digitization.html","title":"Digitization","lang":"en-US","frontmatter":{"sidebarPosition":300},"headers":[{"level":2,"title":"Digitization Quick Start","slug":"digitization-quick-start","link":"#digitization-quick-start","children":[]},{"level":2,"title":"Comprehensive Digitization","slug":"comprehensive-digitization","link":"#comprehensive-digitization","children":[]},{"level":2,"title":"Label Printing","slug":"label-printing","link":"#label-printing","children":[{"level":3,"title":"Printing Header Labels","slug":"printing-header-labels","link":"#printing-header-labels","children":[]},{"level":3,"title":"Print Labels Task","slug":"print-labels-task","link":"#print-labels-task","children":[]}]},{"level":2,"title":"Did you know","slug":"did-you-know","link":"#did-you-know","children":[]}],"git":{"updatedTime":1682459396000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":4},{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":1},{"name":"Tommy McElrath","email":"monotomidae@gmail.com","commits":1}]},"filePathRelative":"guide/Manual/digitization.md"}');export{T as comp,v as data};
diff --git a/assets/events.html-BvhDNAz9.js b/assets/events.html-BvhDNAz9.js
new file mode 100644
index 00000000..254d3f22
--- /dev/null
+++ b/assets/events.html-BvhDNAz9.js
@@ -0,0 +1 @@
+import{_ as e,c as t,o,b as a}from"./app-Bwgh_xIT.js";const n={},r=a('
Every Wednesday, the Species File Group hosts topic-specific meetings currently covering nomenclature, digitization, matrices/observations, technical input, and two open sessions. Questions of any sort are welcome there, regardless of topic. All are welcome.
From time to time we hang out in the evening on Zoom. See the events link above for details.
',8),s=[r];function i(l,h){return o(),t("div",null,s)}const p=e(n,[["render",i],["__file","events.html.vue"]]),m=JSON.parse('{"path":"/about/events.html","title":"Events","lang":"en-US","frontmatter":{"sidebarPosition":20},"headers":[{"level":2,"title":"Weekly","slug":"weekly","link":"#weekly","children":[]},{"level":2,"title":"TaxonWorks Together","slug":"taxonworks-together","link":"#taxonworks-together","children":[]},{"level":2,"title":"TaxonWorks Late-nite","slug":"taxonworks-late-nite","link":"#taxonworks-late-nite","children":[]}],"git":{"updatedTime":1668373922000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":3},{"name":"mjy","email":"diapriid@gmail.com","commits":3}]},"filePathRelative":"about/events.md"}');export{p as comp,m as data};
diff --git a/assets/export.html-Kta3YHgi.js b/assets/export.html-Kta3YHgi.js
new file mode 100644
index 00000000..9a71333e
--- /dev/null
+++ b/assets/export.html-Kta3YHgi.js
@@ -0,0 +1 @@
+import{_ as e,c as a,o as t,b as i}from"./app-Bwgh_xIT.js";const o={},l=i('
You can export a full copy of your database, minus binaries (e.g. images, documents) into PostgreSQL format via the Export project database task. This lets you:
Archive your data
Load it into a local version of TaxonWorks (e.g. running on your desktop)
A quite common data package used for sharing data with biodiversity data aggregators like the Global Biodiversity Information Facility (GBIF) and iDigBio, a Darwin Core Archive (dwca) contains several files (e.g. your data file, a metadata file, and an index file to tell computers reading the package what to expect to find in this specific data package). In TaxonWorks, you can create these packages as needed. To do so, you will use the DwC Dashboard shown next.
Click one of the green buttons in the Download Darwin Core Archive section.
Note your green button options for your dwca file. You may create a dwca for all your data, or a given desired or relevant subset. You can also create your own custom archive (see the Create DwC Archive by filtered collection object result option).
Once you click on an option, generating the file can sometimes take several seconds to create/load, so wait a few seconds, and you will see a result in the next step.
Your download will be queued and built, then available under the Recently created DwC Archives section.
Your export will download as a DWCA, that includes three files (or more) when unzipped:
data.csv (a tab-separated file (TSV) file that can be opened by most spreadsheet programs). This is your downloaded specimen occurrence data.
eml.xml (a metadata file with information about your dataset)
meta.xml (a metadata file that describes the headers included in your dataset).
You can (and will need to) edit your eml.xml file in a plain text editor to prepare it for upload to an aggregator. A sample file that works is available here.
Once you've edited this EML file, make sure to re-package it into a ZIP file.
CAUTION, if using a Mac, the system will add two invisible system files when re-zipping. A workaround is available here: https://perishablepress.com/remove-macosx-ds-store-zip-files-mac/
Once repackaged, add this zipped file to your Integrated Publishing Toolkit (IPT) endpoint. Note there are existing IPT instances that would be happy to host your packaged data. More information on setting one up here:
You can share a zipped copy of the file by generating a link to it. This functionality is turned on if the project administrator has created an API token (See addendum).
Click Generate download
Copy the link generated and share it.
A copy of the Download file is also available for future reference, for a period of 2 days, via the Download data card.
',54),r=[l];function n(s,d){return t(),a("div",null,r)}const h=e(o,[["render",n],["__file","export.html.vue"]]),u=JSON.parse('{"path":"/guide/export.html","title":"Export","lang":"en-US","frontmatter":{"sidebarPosition":62},"headers":[{"level":2,"title":"Full database dumps","slug":"full-database-dumps","link":"#full-database-dumps","children":[]},{"level":2,"title":"Individual TaxonWorks tables","slug":"individual-taxonworks-tables","link":"#individual-taxonworks-tables","children":[{"level":3,"title":"Via \\"Project data overview and download\\"","slug":"via-project-data-overview-and-download","link":"#via-project-data-overview-and-download","children":[]},{"level":3,"title":"Via individual Data cards","slug":"via-individual-data-cards","link":"#via-individual-data-cards","children":[]}]},{"level":2,"title":"CSV","slug":"csv","link":"#csv","children":[{"level":3,"title":"Basic","slug":"basic","link":"#basic","children":[]}]},{"level":2,"title":"Darwin Core Archives","slug":"darwin-core-archives","link":"#darwin-core-archives","children":[{"level":3,"title":"From the DwC Dashboard","slug":"from-the-dwc-dashboard","link":"#from-the-dwc-dashboard","children":[]},{"level":3,"title":"From the Filter collection objects task","slug":"from-the-filter-collection-objects-task","link":"#from-the-filter-collection-objects-task","children":[]},{"level":3,"title":"Preparing your data for an aggregator (e.g. GBIF, iDigBio, ALA)","slug":"preparing-your-data-for-an-aggregator-e-g-gbif-idigbio-ala","link":"#preparing-your-data-for-an-aggregator-e-g-gbif-idigbio-ala","children":[]}]},{"level":2,"title":"Bibliographies (Reference lists)","slug":"bibliographies-reference-lists","link":"#bibliographies-reference-lists","children":[{"level":3,"title":"As CSV","slug":"as-csv","link":"#as-csv","children":[]},{"level":3,"title":"As BibTeX","slug":"as-bibtex","link":"#as-bibtex","children":[]},{"level":3,"title":"Formatted for journals","slug":"formatted-for-journals","link":"#formatted-for-journals","children":[{"level":4,"title":"Create shareable link to your filtered bibliography","slug":"create-shareable-link-to-your-filtered-bibliography","link":"#create-shareable-link-to-your-filtered-bibliography","children":[]}]},{"level":3,"title":"Catalog of Life Data Package (ColDP)","slug":"catalog-of-life-data-package-coldp","link":"#catalog-of-life-data-package-coldp","children":[]}]},{"level":2,"title":"Data matrices (evolutionary, descriptive, quantitative, etc.)","slug":"data-matrices-evolutionary-descriptive-quantitative-etc","link":"#data-matrices-evolutionary-descriptive-quantitative-etc","children":[{"level":3,"title":"Nomenclature stats","slug":"nomenclature-stats","link":"#nomenclature-stats","children":[]}]},{"level":2,"title":"JSON","slug":"json","link":"#json","children":[{"level":3,"title":"Individual records","slug":"individual-records","link":"#individual-records","children":[]},{"level":3,"title":"Via filters","slug":"via-filters","link":"#via-filters","children":[]}]},{"level":2,"title":"The TaxonWorks API","slug":"the-taxonworks-api","link":"#the-taxonworks-api","children":[]}],"git":{"updatedTime":1711747772000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"guide/export.md"}');export{h as comp,u as data};
diff --git a/assets/getting-started.html-RycraOQW.js b/assets/getting-started.html-RycraOQW.js
new file mode 100644
index 00000000..1bc2cf31
--- /dev/null
+++ b/assets/getting-started.html-RycraOQW.js
@@ -0,0 +1 @@
+import{_ as e,c as t,o as a,b as i}from"./app-Bwgh_xIT.js";const n={},s=i('
',4),l=[s];function o(r,c){return a(),t("div",null,l)}const p=e(n,[["render",o],["__file","getting-started.html.vue"]]),d=JSON.parse('{"path":"/guide/getting-started.html","title":"Getting started with some basics","lang":"en-US","frontmatter":{"sidebarPosition":35},"headers":[{"level":2,"title":"In-application help","slug":"in-application-help","link":"#in-application-help","children":[]}],"git":{"updatedTime":1668385163000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":6},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":1}]},"filePathRelative":"guide/getting-started.md"}');export{p as comp,d as data};
diff --git a/assets/glossary.html-h1YJcZRI.js b/assets/glossary.html-h1YJcZRI.js
new file mode 100644
index 00000000..0776abbf
--- /dev/null
+++ b/assets/glossary.html-h1YJcZRI.js
@@ -0,0 +1,6 @@
+import{_ as e,c as a,o as t,b as i}from"./app-Bwgh_xIT.js";const n={},s=i(`
Refers to a geographic distribution record for a taxon listed in a publication. It is “asserted” in the sense that the information is simply taken as given from the publication. If it is “original” it is the first record for that OTU in that place.
A prefix (buffered_) used to indicate verbatim text that is part of a CollectionObject record. Buffered fields are used TaxonWorks in a digitization workflow as the first step of transcribing labels, or images, to digital data. Buffered fields are write-once, they after addition they should not be changed, nor do they track changes to parsed values.
Fields prefixed in cached_ are auto-generated by TaxonWorks based on other values in the record and/or records related to the record. They are used as indicies for searching and for display purposes, particularly cached_<>_html values.
Something that appears similar at the outset (e.g. an Icon), but changes in behaviour or appearance given where and when it is encountered in the application.
In this context, we want to talk about and focus on data fidelity. While we often refer to data quality, we note that in reality, quality as a categorical goal proves quite hard to define. It's subjective and "it depends" on may other factors. With fidelity as the goal, we can seek to ensure the data are as fit as possible (e.g formatted as expected, compliant with relevant standards) and whose completeness can be better understood or visualized. With fidelity as the goal, others can then determine if said data are fit-for-use for their research / data management needs and questions. We recognize and appreciate this considered nuance in terminology as shared by Erica Krimmel at TaxonWorks Together 2024 in our Data Quality Round Table Conversation.
Typing a combination of keys to trigger a behaviour in the UI. Universal hot keys include concepts like ctrl-c for "Copy text to clipboard". TaxonWorks has numerous hot key combinations that speed tasks.
Identifiers distinguish instances, i.e. specific things. TaxonWorks supports many different types of identifiers, and multiple identifiers can be added to individual instances. Some identifier types map 1:1 with physical things like the catalog number attached to specimen in collections, others types are strictly digitial. Some identifiers are Global, some are Local. Global identifiers are those that come from well thought out systems that mint identifiers that are intended to be truly globally (universally) unique. Local identifiers have a user-defined Namespace (the fixed bit of the identifier that doesn't change across the identifier) and a value, which must be unique within that Namespace.
Used in context of tracing text in buffered fields to the verbatim fields include parsed out values. "Naïve" means we anticipate a very simple match, string to string, no fuzziness, no AI, etc.
A “namespace” is the abbreviation for a collection used in specimen accession numbers. For example, in the accession number label USNM 1234567, “USNM” is the namespace. It is not necessarily the same as a repository, as there may be multiple namespaces used by a given repository.
An "object" is an abstract term often used when referencing the representation of a data instance in code. For example, in the underlying code in TaxonWorks there are TaxonName objects, CollectingEvent objects, CollectionObject objects, People objects, etc. We also often speak of adding attributes to objects. In the case of TaxonWorks these additions are called DataAttributes and AlternateValues. In this case we are adding some description to our data-object, for example a name for a "body of water" attribute to our CollectingEvent, or an abbreviation for a term in the tihe title of a Source.
In TaxonWorks parsed values are the formalized representation of the data. For example the verbatim date "12.iv.1997" parsed into three fields in TaxonWorks: start_date_day (12), start_date_month (4), start_date_year (1997).
In TW the parent is the next higher taxon in which the taxon of interest is classified, for example, a genus for a species or a subfamily for a genus. By setting the parent, a curator controls how the classification will appear in TW. For example, for a small family in which subfamilies are not used, the parent of a genus may be a family. In other cases, the parent of a genus could be a tribe. This is determined by the curator. The complete taxonomic history of the taxon’s classification is recorded separately on the Browse Nomenclature screen.
An instance of TaxonWorks supports multiple projects. Each project may have one or more users. Data in one project are only accessible in that project -- with a couple of key strategic exceptions (e.g. "Community" data like source publications that are public, or people names) where data are shared across projects.
“Protonym” in TW refers to a name at the species, genus or family level in its first validly published form. It will always be associated with a literature citation, and it has an author and date, as spelled out by the rules of ICZN. You can think of it as occupying a unique niche in nomenclatural hyperspace. In cases of synonymy, the protonym is not the currently valid name. The currently valid protonym is indicated in many places in by a check mark. However, note that for species names in a taxonomic history, the check mark will indicate the original combination of the name rather than the current one.
A simple means to elegantly suggest changes to a website or code repository by editing a clone of that respository and then sending a message back to the origin that includes those changes. The changes can be considered by the maintainers of the original respostory and integrated, or not.
"Standard operating proceedure." In TaxonWorks this might be a project-specific way of doing things. In TaxonWorks you can assert that some or all of your data was derived from some process by annotating it with a Protocol annotation.
A reference to a digitization process in where all data are laid out for complete capture within an image. TaxonWorks uses stages that have areas defined to match specific types of data, for example "Catalog numbers", "Specimen", "Image registration".
Verbatim fields in TaxonWorks are a small set of CollectingEvent fields that contain parts of the Verbatim or Buffered values. For example given a label like:
USA:TX:Brazos Co.
+Lick Creek Park
+12.iv.1997
+M. Yoder, YPT
+
Then the TaxonWorks verbatim fields verbatim_locality would contain 'Lick Creek Park' and the verbatim_date would include 12.iv.1997.
There are various batch importers available within the UI. These are polished to differing degrees and have various benefits and limitations. The required format, and often an example spreadsheet, is provided in the UI. All batch loaders are two-step, allowing for (and requiring) a preview of results before inserting them into the database.
To explore available batch loaders click on a Data card in the Hub. If batch loader(s) are available then then the batch load link will be enabled.
Batch importers largely target tab-separated text files, though this is not exclusively the case.
Notable batch loaders are found in the TaxonNames, Otus, and Sources data cards, though others exist.
Explore various batch loaders (each data card highlighted in yellow has associated batch loaders at this writing).
See instructions in the UI for expected / accepted data types and format.
Create your own file or use this test file Header column = otu_name Blank lines are skipped Tab-delimited format, UTF-8 encoding, Unix line-endings required
Browse to your file to select it, click preview
If data looks as expected, browse to select that file again and click create.
To upload occurrence data, TW offers the ability to use a DwC Archive file format. For occurrences, the importer is presently limited to vouchered specimen data records.
To use this approach you must have your specimen data in a single spreadsheet-style format that can be export as "CSV".
Preparing for an import follows the following general procedures:
Map your data (provide a column header) for each column of data to be imported
The DwC importer provides flexibility in importing diverse data. These fall in to several types:
DwC terms
User customizable data attributes
User customizable biocuration classes
TaxonWorks' model specific attributes
As headers, these will look like this:
catalogNumber
TW:DataAttribute:CollectionObject:color
caste
TW:CollectingEvent:verbatim_collectors
A DwC term mapping
A user customizable data attribute
A TW biocuration attribute
A TW specific attribute
TIP
A first step is to go through your data and figure out which column header type you'll need. Start by matching to supported DwC terms, then go on from there.
When going from DwC, a flat format, to TaxonWorks your moving your data from rows to Things. We can group the DwC terms into classes to reflect where they end up in TaxonWorks.
It is checked that it equals PhysicalObject before allowing the record to be imported. If the value is empty or term not present it is assumed it is a PhysicalObject
institutionCode
Selects the repository for the specimen that is registered with an acronym equal to this value
collectionCode
Paired with institutionCode it is used to select the namespace for catalogNumber from a user-defined lookup table in import settings, the value itself is not imported.
basisOfRecord
It is checked that it equals an expected valid value for term, e.g. PreservedSpecimen or FossilSpecimen before allowing the record to be imported. If the value is empty or term not present it is assumed it is a PreservedSpecimen [IS THIS STILL TRUE?]
The identifier value for Catalog Number local identifier. The namespace is selected from the namespaces lookup table in import settings queried by institutionCode:collectionCode pair.
recordedBy
It is imported as-is in verbatim collectors field of the collecting event. Additionally, the value is parsed into people and assigned as collectors of the CE. Previously existing people are not used unless the data origin is the same dataset the record belongs to, otherwise any missing people are created.
individualCount
The total number of entities associated with the specimen record (e.g. this record may be for a "lot" containing 6 objects).
sex
Selects the biocuration class from the "sex" biocuration group to be assigned as biocuration classification for the specimen.
preparations
Selects an existing preparation matching the name with this value.
The ISO8601-formatted date is split into start year, month and day collecting event fields. If the value is composed of two dates separated by /, then rightmost date is used as end date and split in the same way as start date. If data contradicts dates from other non-empty date-related terms the record will fail to import
eventTime
Time is split into time start hour, minute, and second of collecting event
startDayOfYear
Using year and the value for this term month and day are calculated and stored in start year, month, and day collecting event fields. If the computed value contradicts dates from other non-empty date-related terms the record will fail to import.
endDayOfYear
Using year and the value for this term month and day are calculated and stored in end year, month and day collecting event fields. If the computed value contradicts dates from other non-empty date-related terms the record will fail to import.
year
The start date year of the collecting event. If the value contradicts dates from other non-empty date-related terms the record will fail to import
month
The start date month of the collecting event. If the value contradicts dates from other non-empty date-related terms the record will fail to import.
day
The start date day of the collecting event. If the value contradicts dates from other non-empty date-related terms the record will fail to import
A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject. If possible, separate the values in a list with space vertical bar space | (known as a pipe). (e.g. Theodore Pappenfuss | Robert Macey)
dateIdentified
The date on which the subject was determined as representing the Taxon. Best practice is to use a date that conforms to ISO 8601-1:2019 see examples.
Selects the nomenclatural code for the taxon ranks used when creating protonyms. The value itself is not imported
kingdom
Creates (unless already present) a protonym at kingdom rank
phylum
Creates (unless already present) a protonym at phylum rank
class
Creates (unless already present) a protonym at class rank
order
Creates (unless already present) a protonym at order rank
family
Creates (unless already present) a protonym at family rank
genus
Ignored. Extracted from scientificName instead
subgenus
Ignored. Extracted from scientificName instead
specificEpithet
Ignored. Extracted from scientificName instead
infraspecificEpithet
Ignored. Extracted from scientificName instead
scientificName
Several protonyms created (only when not present already) with their corresponding ranks and placements
taxonRank
The taxon rank of the most specific protonym
higherClassification
Several protonyms created (only when not present already) with their corresponding ranks and placement. In case a protonym was not already present, only family-group names will be created, names with classsification higher than family-group not previously registered will result in error. Names at genus rank or lower are ignored and extracted from scientificName instead
The DwC importer task includes some TW-specific mappings that are neither DwC core terms nor in any DwC extension term lists but instead, direct mappings to predicates in your projects imported as data attributes for collection objects and collecting events, biocuration groups and classes, and as an advanced-use feature you may have direct mappings to model fields.
WARNING
If submitting an actual DwC-A zip file and not tab-separated text file or spreadsheet, this TW-specific mappings have to be placed as headers in the core table, and not in meta.xml. If you are replacing a mapping from meta.xml, you must make sure to comment it out and also if inserting colums make sure you do the appropriate adjustments to avoid collision.
In cases where you need to import predicate values targetting the imported collection object or collecting event you may do so by naming the column with a pattern like TW:DataAttribute:<target_class>:<predicate_identifier>. <target_class> may be CollectionObject or CollectingEvent, and the <predicate_identifier> may be the either the name of the predicate or its URI. As an example if you have a predicate registered with name ageInDays and URI http://rs.gbif.org/terms/1.0/ageInDays, both TW:DataAttribute:CollectionObject:ageInDays and TW:DataAttribute:CollectionObject:http://rs.gbif.org/terms/1.0/ageInDays can be used to refer to the same predicate.
The importer is able to map sex into the appropriate biocuration group and select the approriate class according to the value. For additional mappings you may use a special column name pattern to select a biocuration group like TW::BiocurationGroup:<group_identifier> where <group_identifier> can be the name of the biocuration group or its URI. In addition the values must match an existing biocuration class and you may use either its name or URI. For example, if you have a biocuration group registered with name Caste and URI urn:example:ants:caste and biocuration class with name Queen and URI urn:example:ants:caste:queen the following examples do all create the same biocuration classification:
Whenever the importer sees that your project has custom attributes for collecting events and/or collection objects that matches Darwin Core URI terms (http://rs.tdwg.org/dwc/terms/<term>), them will be imported as data attributes regardless of any existing mapping of the same field. This allows to preserve verbatim dataaset value for reference as also to import data from terms not supported by the importer.
This is an advance mapping and requires knowledge of the underlying TW models. The pattern is TW:<model_class>:<field> where model can be either CollectionObject or CollectingEvent, and <field> can be the ones listed below.
Think of Predicates as your custom column headers. Predicates are referenced in DataAttributes. Use a Predicate when you want to assign many different values (have rows with many different values) under one heading.
Think of biocuration classes as custom attributes for your collection objects, things like 'male', 'pupa', or 'larva'. These let you assign values useful for your curation of your specimens in a controlled way, ensuring problems like 'M.', 'MALE', 'ale' don't happen in what might otherwise be a "Sex" field. [TODO: reference groups?]. This approach is used when your rows have only a few specific values across the dataset.
Column headers that can't be linked via one of the 3 mechanisms are ignored during the import process. This means its important to do some trial runs in a sandbox, or with a smaller dataset to see that your values are mapping over. The Browse collection object task is a good place to check this.
DANGER
No warning is given when columns do not map, they are simply ignored.
TIP
You can augment your data after import with batch update functionality inside TW. Carefully planning your overal import process can lead to a more efficient overall approach. Sometimes its easier to work in spreadsheets, sometimes within a database.
When first learning TaxonWorks, entering records one-at-a-time offers you the opportunity to learn about more of the features in TW and get a feel for how you and others experience the UI.
For example, you want to enter a specimen record. You have two Tasks enabling you to do this. Choose to use Comprehensive Specimen Digitization Task or the Simple New Specimen Task.
In your project, try creating a simple new specimen record.
Note you will need to select a namespace. You may find you need to add a namespace before you can do this TW task. Adding a value for namespace ensures your uploaded data records will be unique inside your TW project and across TW projects. In your project, you may also need more than one namespace. [Use Tommy’s INHS Insect Collection as an example, with 12 different namespaces that effectively group the various collections housed at INHS ENT].
If you tried the OTU batch loader you can pick one of your OTUs for the name to assign to this specimen.
Add an image if you wish
Select the Preparation type for this specimen. You may need to add a new value to the dropdown using the New preparation type task.
We are in the process of exploring two routes to come from Scratchpads to TaxonWorks.
The DwC import should work well for occurrence data that is based on collected objects.
The SFG team is has worked with a select number of individual Scratchpad curators to script the process of transferring their datadata. Contact us if you are interested in what this approach entails. Note that this process takes programming effort that is a limited resource within the SFG.
',79),d=[i];function s(n,c){return a(),t("div",null,d)}const p=e(r,[["render",s],["__file","import.html.vue"]]),h=JSON.parse('{"path":"/guide/import.html","title":"Import","lang":"en-US","frontmatter":{"sidebarPosition":60},"headers":[{"level":2,"title":"Batch loaders","slug":"batch-loaders","link":"#batch-loaders","children":[{"level":3,"title":"Try a batch loader","slug":"try-a-batch-loader","link":"#try-a-batch-loader","children":[]}]},{"level":2,"title":"Darwin Core Archive (DwC-A) import","slug":"darwin-core-archive-dwc-a-import","link":"#darwin-core-archive-dwc-a-import","children":[{"level":3,"title":"Map your data","slug":"map-your-data","link":"#map-your-data","children":[{"level":4,"title":"DwC term mapping","slug":"dwc-term-mapping","link":"#dwc-term-mapping","children":[{"level":5,"title":"Record-level class","slug":"record-level-class","link":"#record-level-class","children":[]},{"level":5,"title":"Occurrence class","slug":"occurrence-class","link":"#occurrence-class","children":[]},{"level":5,"title":"Event class","slug":"event-class","link":"#event-class","children":[]},{"level":5,"title":"Location class","slug":"location-class","link":"#location-class","children":[]},{"level":5,"title":"Identification class","slug":"identification-class","link":"#identification-class","children":[]},{"level":5,"title":"Taxon class","slug":"taxon-class","link":"#taxon-class","children":[]}]},{"level":4,"title":"TaxonWorks mappings","slug":"taxonworks-mappings","link":"#taxonworks-mappings","children":[{"level":5,"title":"Mappings to project predicates","slug":"mappings-to-project-predicates","link":"#mappings-to-project-predicates","children":[]},{"level":5,"title":"Mappings to biocuration groups and classes","slug":"mappings-to-biocuration-groups-and-classes","link":"#mappings-to-biocuration-groups-and-classes","children":[]},{"level":5,"title":"Mappings to DwC predicates","slug":"mappings-to-dwc-predicates","link":"#mappings-to-dwc-predicates","children":[]},{"level":5,"title":"Direct mapping to TW model fields","slug":"direct-mapping-to-tw-model-fields","link":"#direct-mapping-to-tw-model-fields","children":[]}]}]},{"level":3,"title":"Configure TaxonWorks for your DwC import","slug":"configure-taxonworks-for-your-dwc-import","link":"#configure-taxonworks-for-your-dwc-import","children":[{"level":4,"title":"Namespaces","slug":"namespaces","link":"#namespaces","children":[]},{"level":4,"title":"Controlled vocabulary terms","slug":"controlled-vocabulary-terms","link":"#controlled-vocabulary-terms","children":[{"level":5,"title":"Predicates","slug":"predicates","link":"#predicates","children":[]},{"level":5,"title":"Biocuration classes","slug":"biocuration-classes","link":"#biocuration-classes","children":[]}]}]},{"level":3,"title":"Unmapped columns","slug":"unmapped-columns","link":"#unmapped-columns","children":[]}]},{"level":2,"title":"Drag and drop","slug":"drag-and-drop","link":"#drag-and-drop","children":[]},{"level":2,"title":"Record by record","slug":"record-by-record","link":"#record-by-record","children":[{"level":3,"title":"Try Simple New Specimen","slug":"try-simple-new-specimen","link":"#try-simple-new-specimen","children":[]}]},{"level":2,"title":"Coming from other software","slug":"coming-from-other-software","link":"#coming-from-other-software","children":[{"level":3,"title":"Scratchpads","slug":"scratchpads","link":"#scratchpads","children":[]}]}],"git":{"updatedTime":1712614078000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":3},{"name":"Deborah Paul","email":"dlpaul@illinois.edu","commits":1}]},"filePathRelative":"guide/import.md"}');export{p as comp,h as data};
diff --git a/assets/index.html-B6PPCidR.js b/assets/index.html-B6PPCidR.js
new file mode 100644
index 00000000..b66e825f
--- /dev/null
+++ b/assets/index.html-B6PPCidR.js
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+import{_ as e,c as t,o,b as a}from"./app-Bwgh_xIT.js";const i={},n=a('
To see this vision realized we need dedicated collaborators (developers, work-bench experts, labs) and funding, i.e. the Species File Group and its current collaborators does not presently have these advances as targeted milestones, nor do they anticipate significant code-contributions from "core" members in the absence of said collaborations/funding. The SFG is very open to guiding work done in this area, i.e. facilitating developers and data-modellers and providing parallel work in some areas, for example implementing externally developed, well thought out, UIs.
At present managing Sequence data is within the purview of TaxonWork's "vision" in the following ways (we're an open community, this can evolve):
Sequence handling in TaxonWorks is envisioned as leaning towards long-term vouchering alongside simple sequence annotations (think biodiversity informatics focused on taxonomy) as opposed to more complex annotation systems (e.g. complex structural annotations, functional graphs, etc.).
TaxonWorks contains excellent CollectionObject and Extract management capabilities, i.e. the framework for vouchering the physical origin of sequences is well developed. This in-and-of-itself, particularly in combination with the extensible functionality offered by customizable data-attributes may fill a gap within molecular labs.
TaxonWorks has a Sequence model, and some nice back-end functionality work has been done on it, for example we added a logic-based (and/or) description framework for linking one sequence to another (think primers, blast reference sequences, etc.)
There is a nice Descriptor context that treats Sequences as just another column type, i.e. there are excellent inherent capabilities for mixing molecular and morphological data and exporting unified datasets for analysis.
While Sequence objects can be created in the UI functionality therein is primitive and has not been used "for real", i.e. the UI/UX needed for actual practical day-to-day work does not exist (2024/1/26)
Sequences managed in TaxonWorks should be curated and have some human-asserted metadata. For example we're not aiming to manage raw-reads, or unassembled data.
Sequences are stored as raw strings, not in a BLAST database, it is of course conceivable to change this back-end storage should advantages in indexing and storage size be needed in the future.
Storing genomes (unassembled or assembled) is not presently a goal. Linking vouchers to metadata about a genome is fully in scope.
We know of many systematics labs where 10k x 4k matrices (terminals by genes) are now the targets of research efforts. We know of no system that comprehensively manages this type of project, for example tracking gaps in required target specimens or genes as projects progress. This is the initial maximum size we envision fitting within a TaxonWorks framework.
We understand the basic starting points (annotated FASTA files) for large-scale integrative taxonomy (LIT). Combining an entry point that starts data management with an annotated FASTA file and then lets users advance their species concepts through the powerful means of exploring their data with existing (and novel) querying is very much in the scope of our vision. Single barcode-style sequences for 100s of thousands of specimens / project is well within our vision.
Analysis of sequence data should be done outside TaxonWorks, being facilitated by API endpoints and exports manageable inside TaxonWorks. For example once Sequence data are present you can not use TaxonWorks to trigger an alignment (though calculating some simple distance metrics are desirable for filtering data in LIT contexts).
We have done prior work in managing full Sanger-sequencing workflows (PCRs, worksheets, etc.). This code is in the precursor project mx. It may be relevant to some.
No well tested batch loading functionality exists. Simple FASTA processing should be very straightforward. Thanks to the scripting framework that comes with TaxonWorks the software is very well positioned to facilitate custom 1-off migrations.
We very much would like to facilitate the export to NCBI/repository framework based on data captured in TaxonWorks.
',8),s=[n];function r(l,c){return o(),t("div",null,s)}const h=e(i,[["render",r],["__file","index.html.vue"]]),m=JSON.parse('{"path":"/guide/FAQs/","title":"Introduction","lang":"en-US","frontmatter":{"sidebarParentPosition":100},"headers":[{"level":3,"title":"How do I contribute back to the community?","slug":"how-do-i-contribute-back-to-the-community","link":"#how-do-i-contribute-back-to-the-community","children":[]},{"level":3,"title":"What about sequence and genomic data, how do they fit into TaxonWorks vision?","slug":"what-about-sequence-and-genomic-data-how-do-they-fit-into-taxonworks-vision","link":"#what-about-sequence-and-genomic-data-how-do-they-fit-into-taxonworks-vision","children":[]}],"git":{"updatedTime":1706297562000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":7},{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":1}]},"filePathRelative":"guide/FAQs/README.md"}');export{h as comp,m as data};
diff --git a/assets/index.html-B_Sr65y4.js b/assets/index.html-B_Sr65y4.js
new file mode 100644
index 00000000..8c50010d
--- /dev/null
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+import{_ as e,c as t,o}from"./app-Bwgh_xIT.js";const a={};function i(s,r){return o(),t("div")}const l=e(a,[["render",i],["__file","index.html.vue"]]),d=JSON.parse('{"path":"/","title":"Home","lang":"en-US","frontmatter":{"home":true,"title":"Home","heroImage":"/images/taxonworks_home.svg","actions":[{"text":"Guide","link":"/guide/","type":"primary"},{"text":"Develop","link":"/develop/","type":"primary"},{"text":"About","link":"/about/","type":"secondary"}],"features":[{"title":"Guide","splash":"Learn to use TaxonWorks","details":"Get the big picture. Start a project. Get started. Study manuals, watch videos, get tips, learn best practices from SOPs, answer \\"How do I?\\" from FAQs, mobilize data with import and export, conect workflows with the API. Request features, file bug reports."},{"title":"Develop","splash":"Learn to develop TaxonWorks","details":"Install, design, code, and document TaxonWorks. Find source-code, data-models and technical documentation. Issue tracking. Build this site!"},{"title":"About","splash":"Learn more about TaxonWorks","details":"Contact and connect with the community. Understand who TaxonWorks is for. Cite the project. Find users, their data, and examples of use. Read about its past, present and future. More about biodiversity informatics."}],"footer":"Content is CC0. Please consider citation.","footerHtml":true},"headers":[],"git":{"updatedTime":1663604848000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":2},{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":2},{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"README.md"}');export{l as comp,d as data};
diff --git a/assets/index.html-BaZZjf64.js b/assets/index.html-BaZZjf64.js
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index 00000000..247eb336
--- /dev/null
+++ b/assets/index.html-BaZZjf64.js
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+import{_ as e,c as o,o as i,b as n}from"./app-Bwgh_xIT.js";const t={},a=n('
Our vision is a world in which the descriptions of Earth's life permeates humanity.
Our mission is to make TaxonWorks, and its companions, as excellent as those that describe life on Earth. As the requirements, needs, and goals for those that describe life evolve, so too should the resources and tools that facilitate their work.
Here in docs.taxonworks.org, everyone contributes to the content, development, and evolution of TaxonWorks' documentation. Click where you see "Edit this page" to offer new information and update existing content.
',8),s=[a];function r(d,l){return i(),o("div",null,s)}const h=e(t,[["render",r],["__file","index.html.vue"]]),m=JSON.parse('{"path":"/guide/","title":"The big picture","lang":"en-US","frontmatter":{"sidebarParentPostion":10},"headers":[{"level":2,"title":"Vision and mission","slug":"vision-and-mission","link":"#vision-and-mission","children":[]},{"level":2,"title":"Everyone included","slug":"everyone-included","link":"#everyone-included","children":[]}],"git":{"updatedTime":1668392731000,"contributors":[{"name":"mjy","email":"diapriid@gmail.com","commits":4},{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":3},{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":1}]},"filePathRelative":"guide/README.md"}');export{h as comp,m as data};
diff --git a/assets/index.html-BoUmPZh2.js b/assets/index.html-BoUmPZh2.js
new file mode 100644
index 00000000..e93a6f69
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+import{_ as a,r as n,c as i,a as e,d as o,e as s,w as r,o as c}from"./app-Bwgh_xIT.js";const d={},l=e("h1",{id:"introduction",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#introduction"},[e("span",null,"Introduction")])],-1),u=e("p",null,[e("em",null,"In these next sections you'll find detailed instructions and examples of how-to scenarios in TaxonWorks, sometimes from the perspective of a specific projects needs.")],-1),m=e("p",null,"With this manual we break down TaxonWorks into sections by different pivot points. For example, once you've understood the basic interface of TW, you may want to focus on given areas of interest such as managing your source data or your images or creating a matrix or entering data as part of your digitization efforts.",-1),f=e("p",null,"Of course, you may also want to focus your work around a particular process instead such as filtering existing data to create a subset of records for download or for verification and editing.",-1),p=e("p",null,"What follows next are sections dedicated to how-to for specific major functions of TW and to processes available.",-1);function h(_,g){const t=n("RouteLink");return c(),i("div",null,[l,u,m,f,p,e("p",null,[o("Note in the "),s(t,{to:"/guide/community-resources.html"},{default:r(()=>[o("Community Documentation")]),_:1}),o(' section you can find examples of entire manuals written for a specific group managing their project data in TW as well as workflows and protocols for how they manage specific tasks in TW (aka "standard-operating-procedures").')])])}const w=a(d,[["render",h],["__file","index.html.vue"]]),y=JSON.parse('{"path":"/guide/Manual/","title":"Introduction","lang":"en-US","frontmatter":{"sidebarParentPosition":40,"sidebarPosition":10},"headers":[],"git":{"updatedTime":1660851576000,"contributors":[{"name":"Debbie Paul","email":"dlpaul@illinois.edu","commits":4},{"name":"mjy","email":"diapriid@gmail.com","commits":1}]},"filePathRelative":"guide/Manual/README.md"}');export{w as comp,y as data};
diff --git a/assets/index.html-CJG0iPrK.js b/assets/index.html-CJG0iPrK.js
new file mode 100644
index 00000000..1b42cb04
--- /dev/null
+++ b/assets/index.html-CJG0iPrK.js
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+import{_ as e,c as a,o,b as r}from"./app-Bwgh_xIT.js";const s={},n=r('
¿Por qué enfatizar que el desarrollo de software en la ciencia es importante en términos generales? ¿Cómo se describen aquí los recursos disponibles para los desarrollares?
Un proyecto de la naturaleza de TaxonWorks necesita contribuciones de muchas personas para mantenerse en el tiempo. Para este fin, trabajamos arduamente en construir una base que permita y aliente a cualquier persona a contribuir con el proyecto. Los puntos detallados incluyen:
Todos los elementos del proyecto son de codigo abierto.
Existen ejemplos de meta-proyectos, por ejemplo taxonowrks_stats (demo) que ilustran como construir una aplicación a partir de la API.
TaxonWorks cuenta con generadores de codigo que le permiten crear una nueva tarea o un cargador por lotes en una sola linea.
TaxonWorks está construido en Rails. Las convenciones aqui actuan como un marco de las catacteristicas que pueden ser escritas en Ruby u otros framework de javascript como Vue.
TaxonWorks está sometido a pruebas unitarias. Esto significa que puede contribuir sin miedo a romper algo.
TaxonWorks utiliza Kubernetes para el despligue en producción.
El Species File Group y sus miembros han realizado hackatones y muchos talleres conjuntos. Pongase en contacto si está interesado en participar en estos. También están interesados en apoyar visitas a posibles desarrolladores, estudiantes. Tambien estan interesados en apoyar la visita de posibles desarrolladores, estudiantes o cualquier otra persona que desee obtener un bootcamp en el desarrollo de TaxonWorks
Las imagenes de Docker le permiten desarrollar a traves de la API utilizando un framework de JavaScript con una minina configuración.
',5),t=[n];function i(l,c){return o(),a("div",null,t)}const p=e(s,[["render",i],["__file","index.html.vue"]]),u=JSON.parse('{"path":"/es/develop/","title":"El panorama general","lang":"es-ES","frontmatter":{"sidebarPosition":10},"headers":[{"level":2,"title":"¿Cómo apoya TaxonWorks las contribuciones de los desarrolladores?","slug":"¿como-apoya-taxonworks-las-contribuciones-de-los-desarrolladores","link":"#¿como-apoya-taxonworks-las-contribuciones-de-los-desarrolladores","children":[]}],"git":{"updatedTime":1677462190000,"contributors":[{"name":"José Luis Pereira","email":"pepelui@outlook.com","commits":1},{"name":"jlpereira","email":"pepelui@outlook.com","commits":1}]},"filePathRelative":"es/develop/README.md"}');export{p as comp,u as data};
diff --git a/assets/index.html-CKgkt9my.js b/assets/index.html-CKgkt9my.js
new file mode 100644
index 00000000..74cc4ba5
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Addresses the questions: "What does the data-store in TaxonWorks look like, and what is the thought process behind its development? Who are the target audiences for these docs?"
To understand the data model used in TaxonWorks, in addition to the discussion below, there are series of linked resources here.
Graphical entity-relationship ("ER") figures. We use er in the "modelling a domain sense", not particularly a 1:1 description of the links between model and database (though there are numerous times where this is the case). Algorithmically drawn, their purpose is to provide an overview of how data in TaxonWorks are modelled at a generalized level. To draw these figures certain constraints are used, this means that they are cleaner looking, and not cluttered, but also that they may not completely illustrate all pertinent entities or relationships as defined for that model. Follow the er links or see the Model section. Most nodes can be clicked to navigate onwards.
A description of the database table for each model. Tables are named as seen in the headers. Many (but not all) related tables are linked in the column name. Follow the table links or see theTables section.
A text description of each model/class. This is provided in the context of the code for that model on a separate website. That website is generated with each code commit, it includes the full documentation for the TaxonWorks code-base, so it is easy to get lost for the uninitiated. Follow the rdoc links from the respective tables and models. Using this site as a basis for exploring rdoc can keep you from getting lost therein.
Direct links (api) to the resources behind the models as represented by TaxonWorks external facing API. For now see documentation at https://api.taxonworks.org. Some models do not yet have a corresponding resource. Some models properties and attributes are accessible by related API endpoints.
There are various target audiences for this information, some served more than others. TaxonWorks users may belong to more than one of these roles, they are not exclusive of one-another. With some small exceptions no one resource here fully meets the needs of these audiences, but with a little imagination they have a role. Those who might make use include:
',6),u=n("
Developers - The obvious target group. All resources (er, table, rdoc, api) are routinely referenced during development
TaxonWorks' scientists - TaxonWorks has many facets, browsing the er diagrams can illuminate data types that you might not have known existed, or give you a better understanding of how some of interfaces relate to one-another
Scientists migrating or evolving personal databases - Perhaps looking for how they might migrate their data into TaxonWorks, table documentation is a potential start for those who seek to migrate their data by scripts
Ontology curators - While not a true ontology, many of the models illustrated in the er must be represented in ontologies and all need to be abstracted if ontologies are to represent core needs of biodiversity informatics
Standards builders - Software and tools guide standards development, and vice-versa. Because standards take a long time to develop tools often "predict" what might need to be standardized. Tools may directly implement standards or serialize to them. All of the entities, and their attributes here, potentially contribute to the broader standards discussion.
High-level data modellers - E.g. those considering archival or indexing resources, er diagrams self-describe their domain, and can be used to get a quick over-view of the kinds of data that data-aggregators might need to integrate at a broader scale
Students - Students are perhaps first exposed to taxonomy via specimens in natural history collections, reading papers in print, and in their course work or textbooks. There is whole layer of data-science (biodiversity informatics) behind taxonomy, the illustrations and documentation here can act as a resource for learning about how we describe and classify the Earth's species.
",7),p=e("strong",null,"Scientists",-1),m=e("a",{href:"https://api.taxonworks.org",target:"_blank",rel:"noopener noreferrer"},"API",-1),g=e("li",null,[e("strong",null,"Semantic web enthusiasts"),t(" - A challenge is to turn the generalized "),e("code",null,"er"),t(" models into RDF, for example how might we see TaxonWorks data in "),e("a",{href:"https://www.wikidata.org",target:"_blank",rel:"noopener noreferrer"},"Wikidata"),t("? This challenge shares many concerns with ontology builders. What are the universals? Properties? Classes?")],-1),f=e("figure",null,[e("object",{data:"/images/model/data/specimen_object_graph_eg1.svg",type:"image/svg+xml"}),e("figcaption",null,' An "object graph", exported from TaxonWorks for a collection object, illustrating a serialization of TaxonWorks that begins to approximate that required in RDF representations. Notice Identifiers (orange triangles), People, Names (pink squares) and Taxon Concepts (green hexagons) are all their own classes of data, among numerous other types. The figure layout was post-processed in Illustrator. ')],-1),b=e("h2",{id:"concepts",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#concepts"},[e("span",null,"Concepts")])],-1),_=e("p",null,[t("At its core TaxonWorks' data model is a handful of straightforward, yet broad "),e("code",null,"core"),t(" concepts (orange rounded ovals below):")],-1),v=e("code",null,"annotations",-1),w=e("code",null,"supporting",-1),y=e("code",null,"core",-1),k=e("figure",null,[e("object",{data:"/images/model/er.svg",type:"image/svg+xml"}),e("figcaption",null," Key data classes in TaxonWorks. 1) Nodes. Orange, rounded rectangles: 'core' data; light-blue rectangles: 'supporting' data; blue ovals: 'annotators'x. 2) Edges. Solid lines: key relationships; dashed lines: examples, i.e. not all relationships to the class being pointed at are shown. Arrows point to the many side of the relationship, for example one OTU has many Identifiers. Click to navigate to that class. ")],-1),x=e("h2",{id:"meta-model",tabindex:"-1"},[e("a",{class:"header-anchor",href:"#meta-model"},[e("span",null,"Meta-model")])],-1),T=e("p",null,'TaxonWorks uses an "ontology-based, graph-aware, relational database" approach to representing and storing data. Practically, this means several things:',-1),D=e("li",null,[t("Each "),e("a",{href:"/develop/Data/tables.htm"},"data table"),t(' corresponds to a class of data. A record in that table asserts that an single instance of that class exists. This is the "Ontology" bit.')],-1),W=e("code",null,"TaxonName",-1),S=e("code",null,"TaxonName",-1),j=e("code",null,"taxon_names",-1),A=e("code",null,"BiologicalCollectionObject",-1),O=e("code",null,"Specimen",-1),C=e("code",null,"BiologicalCollectionObject",-1),q=e("code",null,"type",-1),z=e("code",null,"
