About Sources in TW
Discover the Source (e.g. publications) management features of TaxonWorks here. For example, sources are shared across projects, a cool time-saving community feature of TW.
Credit: much of the following information derived from a manual tailored for and written by the Universal Chalcidoidea Database (UCD@TW) Project community.
The Source Hub
In TaxonWorks, sources include the literature database, citations, and other content that is fed directly into the database. The easiest way to access sources is through the Source hub
task. This is a unifying task that combines several commonly used tasks associated with sources. As a curator, researcher, data manager, student, or technician you may primarily be working from sources that are published papers. Source data can be entered one record at-a-time field-by-field or using BibTeX or CrossRef DOIs. From most reference manager software, one can export source information in the BibTex format and edited as needed in any regular text editor. This can be used for uploading source
data into TW. With this wiki, you can learn more about BibTex.
Source hub
user interface sections
Source hub
task features
Source hub
sections offer select, filter, recent sources, add new source, and batch upload. The Select a source
option offers a smart selector so you only need to enter as many letters needed to uniquely identify a source. For example, the string 'wool dal sig' brings up Woolley and Dal Molin (2017). If a source is found it will show beneath the search box.
- Type information in
Select a source
to see if a source is in the database.- If you click on a result in the popup beneath the search box, it will take you to a page describing the source.
Legend: Source hub
search result
- If you click on a result in the popup beneath the search box, it will take you to a page describing the source.
- With
Filter sources
you can apply different search criteria to locate sources of interest.- Use this feature to identify sources you want to work on.
My recent sources
shows a list of sources that you have entered recently.New Source
takes you to a screen that enables you to add new sources using various methods.- Note the
Batch upload
option here via BibTeX formatted source data.
Related Source Tasks
Next we delve into the details of various work you may need or want to do with source information (e.g. adding sources, editing, tagging, and filtering). The source content needing to be captured includes such data as new taxon names, people strings or names, distribution information, type information, and biological associations. For efficient source data extraction and entry, we recommend familiarity with the following TW Tasks and Data Cards.
FUTURE LINK TO INFORMATION about each of these items
Tasks | Data Cards |
---|---|
Browse nomenclature | Taxon names |
Browse OTUs | Biological Associations |
Source hub | Sources |
Filter sources | Manage Controlled Vocabulary Terms |
New taxon name | |
New type specimen | |
New combination | |
Uniquify People |
Source Show
Once you find the publication of your choice using the Source Hub
, clicking on it opens the Show
page. Here you will find various ways to navigate to related information and a path to Edit
this source record. Next we describe some of the features and functions found in the Source show.
Note the green Pinboard icon
at the upper right. Clicking this adds the source to your Pinboard for quick access.
The Radial Annotator
is a very common function used throughout TW. It provides convenient access in one place to a variety of relevant functions. For example, clicking on the
Radial Annotator
for a givenSource
might look like this:
Radial Annotator
functions
Documentation
is where you can drop a pdf of the source, or supplementary files.Tags
allow you to mark sources for later with tags such asSource Unprocessed
, orSource Processed for Nomenclature
. Instructions on creating and editing Tags are included below.Notes
is a free text field for any information you might want to add.Identifiers
provides a place to store one-to-many identifiers for a given object. For example, a paper might have a globally unique digital object identifier, aka DOI, but also an author-assigned identifier.Data attributes
in TW gives you a place to store your unique data that may not fit in any typical TW field currently in the data model.
Try Editing a Source
- From the
Source Hub
search to a publication you choose - Click
Edit
to open the task to make corrections or put text in title in italics, for example.
Note that italics are indicated in BibTex format as follows <i> text </i>
. Everything in between the special symbols will display or print in italics. There are tools in TW to do this for you by selecting text and hitting a button.
- Be sure to click the
Save
button to keep any changes.
HINT: In Edit
, you see New source but you started by clicking the Edit
option from an existing source. Rest assured this New source window does not mean duplication of the source.
Adding a Source
About adding Sources, options offered here include the option to re-order fields and ways to auto-fill the Source
information using a CrossRef DOI
or using BibTeX you may generate from Zotero or EndNote. This section features commonly used fields. See the scenarios section to find related activities that fit your workflows.
- First, using the
Source hub
always check to be sure the source is not already in TW. If it isn’t found in the search box in the Source Hub, '—None—' will appear below it. With TW "smart" searches you need only provide enough minimal text to find the source (e.g. misspellings may cause you to miss a source). - Clicking
New Source
in theSource Hub
brings up this screen.
Sortable fields
box in the upper right.
- The yellow triangle means you have made changes that have not been saved.
- Be sure to
Save
before you leave this screen, or changes will be lost. - If you have the DOI for a new source, this button provides access to the CrossRef database of DOIs. If it works (it usually does), most of the fields you need will be filled in. Be sure to check them, as they are not always correct.
- If you have the reference in BibTex format (most reference databases will output this), you can input it here.
- From Zotero, simply select the reference, right-click on it, select "export item" and save the file as BibTeX.
- From EndNote, select the reference and fill out the "label" field. Then go to File > export and select "text file", "BibTeX export". Most people don’t fill out the "label" field in their EndNote database, but if you don’t, you will have to add the label manually by editing the exported text file (that is the field highlighted in the example below).
- In the
New Source Form
, Choose the blueBibTex
box at the top of the screen, and paste in the exported *.txt file. (No drag and drop here).
Most of the fields may be self-explanatory. Here we note a few tricks, for instance:
Entering an author name in this box (5)
Authors
tries to pull it up from the table of known authors. If it isn’t found, you can use theAdd New
button that appears in this case. This is an advantage in some situations over entering authors as verbatim text (in the Verbatim from BibTex field lower in the screen), because you can easily pull them up later, for example, when adding author names to new species.Similarly, below the
Author
section is a search box forSerials
(journals). If the journal is not found, look for theNew
button to the right of the Serial screen. This opens a screen for you to add a serial to the serials table.Once you have created the new source, you should go to
Documentation
in the blueRadial annotator
to the right of theSource
and upload the PDF file if available.(Optional) Use the TW
Tag
feature to group and track which papers need data parsing or do not.- To do this go to the Tags choice in the
Radial annotator
- Tag the source as desired (e.g.
Unprocessed
) - And add other suitable tags such as
No Nomenclatural Acts
orNomenclatural Acts
as appropriate (this is specific for the UCD project, other projects may use different tags).
- To do this go to the Tags choice in the
If a source has a title in a language other than English, and you wish to enter the English translation (or translation in any other language), follow these steps:
- Enter the source with the title as given in the paper and create it.
- Click on the blue
Radial BibTex annotator
to the right of the source at the top of the page, and click on the pie slice forAlternate Values
. - Choose title from the pick-list, the language for the translated title, and paste the translation in the Value field.
- Be sure to
Save
it (green button) if this is a new source. Then the original title and translation will both be rendered.
As all fields are present on the data entry screen for all types of sources, it can be a bit confusing, particularly for books and chapters in books. The article type for a chapter in a book is "Inbook", and the book title would go into the Booktitle field. For books, there are fields for Editors, Series (if needed), Booktitle, Publisher, and Address (usually city or city and country). The type of a technical report is "techreport".
PDFs for Sources
Using the UCD@TW Project as an example, note that most screens that pull up lists of sources in TW have a convenient PDF icon that either opens the source in the PDF viewer (where you can download it), or enables you to download it directly to your browser. For example, if you pull up a source using the Source hub
, you will get a screen like this -- the so-called Show
page. The pdf icon will open the source in your browser.
Source
has PDF
You can also check to see whether a pdf has been associated with a source using the Radial Annotator
associated with that source.
- Click the
Documentation
wedge in theRadial Annotator
to get the screen below. - If a pdf for the source is not present, drag and drop it into the box as shown.
- If a pdf is associated with the source, you can click the icon indicated by the red arrow to download to your browser.
Source
have a PDF?
Tags on Sources
Tags
in TW provide a unique way to group documents (or other objects in TW) in any way that you choose. With the keywords
that you put into a tag, you and colleagues can find the relevant materials needing work or find groups where work is complete and may need vetting.
UCD@TW Project Tag Example
Because UCD@TW is a community-curated database, they added keyword tags for sources that allow them to better organize and coordinate group work. These are the tags currently associated with their sources. Tags can be added or removed from a source in the Radial Annotator
. Most of these tags should be self-explanatory.
- HINT:
Keywords
are the words you put in aTag
. - If certain that a source is an
early view document
, that is, not yet published, they add this tag as any nomenclatural acts in the source are not yet valid. - If the source is new to TW, for now, they use the tag
Source unprocessed
, as this allows other curators and helpers to pull up sources that need to be curated. - And to anyone starting work to curate a paper, they apply the tag
Source being processed
so that other community members will not try to work on it simultaneously.
HINT: Using the Browse Annotations
task you can find out who has claimed sources (or assigned various tags).
Creating or Editing Tags
Using the Manage Controlled Vocabulary task (shown below), you can create custom tags
with the keywords
of your choice. In this task, you will need to decide the keywords to use, enter them, and define what they mean.
Manage Controlled Vocabulary task
- To create a new tag use the
Name
,Definition
, andLabel color
fields on the left of the screen. - Note that the definition field must have at least 20 characters before the
Create
button is clickable. - Note that if you want to use the same color for multiple tags, you can use the eyedropper tool in the
Label color
window. - To
Edit
an existing tag, use the green iconassociated with the
Tag
.
Sources With Versions or Translated Titles
Some sources exist in more than one version, either with translated titles or in entirely translated versions. To add a translated title, use the radial annotator, under "alternate values", and add the information under "title" to add the English version, such as in the case below:
Example Paper With Title in German and English
Note, there are at least two reasons why you might have more than one version of source:
- Someone has done a translation of a paper, but it has not been published separately. In this case, simpy add the translated pdf as a second document to the source (Documentation tool in Radial Annotator).
- The translation has been published separately from the original source. A common example is Entomological Review, which is a parallel version of Entomologicheskoe Obozrenie published in English. In this case, the page numbers are likely to be different in the two journals. You should enter this as a separate source from the original paper in Russian. A search on the author and date will bring up both sources.
Filtering Sources
TW employs a powerful utility to search for particular sources, the Filter Source task
. Among the search fields, which can be used in any combination, are the following:
Keywords
: search text or title. These are verbatim text search fields that will scan the title or other text fields for keywords, such as taxon names. However, if the name is not in the title, it may not get picked up.Authors
: self explanatory. Search for authors verbatim or for authors in the Authors data table.Date
: you can provide starting and ending years for the search.Tags
: If a source has been tagged, you can search for the tag(s) here.- You can batch tag sources using the method described below.
- (UCD@TW specific note: However, this will apply mostly to literature that has been added since the transfer of sources from UCD@NHM to UCD@TW).
Topics
: This is one of the potentially most powerful uses of this utility. All of the tags to citations from UCD@NHM (the original UCD in London) should have been carried over to UCD@TW on import. Thus, UCD@TW folks can search for papers containing host information, keys to species, redescriptions, or any of the topics in the Topics list. Note that if you have Topics in your pinboard, they will appear here if you select Pinboard. Or you can Search for a topic or pull up the entire list of topics using All.
Once you have created a list of sources, you can do the following:
Select All
(button is at top left) orSelect Individual Sources
.Tag
: once you have selected sources you can tag them using whatever tag or tags are in your pinboard by hitting the greenTag
button. If there is more than one tag indicated as the default in your pinboard, both will be added. Note that if you create a new tag (explained above) this automatically becomes the default tag in your pinboard.- HINT: This is a powerful way to create groups of sources for particular projects.
- Download CSV: this creates and downloads to your browser a comma-delimited data file.
- Download formatted: here you have the option to choose a format style (e.g. Zootaxa) and create a formatted bibliography.
- If a pdf is associated with the source, you can capture it using the pdf icon.
Importing
One at a time
Batch Upload
Using the Batch Upload
section of the Sources
Data tab from the project home screen, you can upload a list of BibTex-formatted references all at once.
From this screen, you can upload a Bibtex formatted TXT file that will allow for import of your references. Use this to load bibliographies exported from tools like EndNote, or Zotero. An example file is available here. Your Bibtex file must meet the following conditions:
- The file to import should be in UTF-8 encoding.
- The file should have unix style line-endings.
- All entries should include a populated 'Label' field containing a unique internal identifier for the record. Endnote does not provide this by default, Zotero does.
Year fields should not include periods ('.'). Try using a BibTeX bibliography "linter" or validating tool (for example) on the web to find errors in your file.
Once you upload, you will see a preview list of your sources, highlighted in green, brown, and red. Green references will be imported, brown ones will be imported but have some soft validation that should be cehcked or fixed before upload, and red ones will not be imported.
Once you've ironed out any problems, you need to re-upload your data using the Choose File
button.
Click the Create
Button to upload your sources. Once the upload finishes, you should get a screen like this: . You can click the edit buttons or search for them in the
Filter Sources
task.
Exporting
- CSV
- in a custom format
Source Scenarios (aka How-To)
When getting data from publication sources into TW, many "how-to" questions may arise. Please see next the following common situations and how to proceed for each. Each of these examples offer you an opportunity to try it yourself in your sandbox account.
Find uncurated papers
Say you want to find new sources (papers) that have not yet been curated. The easiest way to do this is to use the Filter Sources
task. For example, if you enter the family name in both Search Text and Title
, and Source unprocessed
in Tags, you will generate a list of currently uncurated papers for that family:
[INSERT SCREENSHOT]
The tag
box allows you to create collections of sources, for example, to download as *.CSV files for your own spreadsheet or database.
The PDF icon
opens the source
in the source viewer
, from which it can be downloaded. If no PDF is associated with the source, the PDF icon will not show. You will need to find a pdf for the source outside of TW, and add it using the Radial Annotator
, as shown above.
Note that there is a red button to remove from project
. This is because references are SHARED across projects in TaxonWorks, that is, if someone outside UCD already created this source record, you should be able to simply add it. Note that reference data for sources are shared, but not PDFs.
The blue buttons to the right are the BibTex Annotator
for sources, described above, and the Navigate Radial
(looks like a compass arrow), which brings up various functions, including an edit slice which takes you to the source editor.
Document information from a newly published source
When a new source (paper/book/etc.) is published and you want to document the information it contains, note the following steps.
(Historically, this workflow is described in-depth as an exercise in the former documentation repository in "basic_article_parsing.md" which you can find in Other Documents from the left sidebar).
- Go to the
Source Hub
task card, search the sources in TW to see if it exists. - If it doesn’t then create it, preferably using
CrossRef
function (blue icon at top ofNew Source
Screen) as described above. We recommend usingCrossRef
because it imports more metadata (BibTeX
e.g. from Google Scholar keeps fields to a bare minimum). - If it is in the database but has not been processed, this will be indicated in the
Radial Annotator
undertags
. Always be careful since automatically imported articles, even if they are recent, may have wrong data. For example, the year informed by the web site may not match the year of publication (usually explicitly stated in the PDF file). - Also, see immediately above for instructions on using the
Filter Sources
task.
Add new taxon name
For this task, be sure you have put the source
in the Pinboard
and selected it as the default
, as this will save a lot of time during the process. To manually create a new taxon name (e.g. species / genus / family):
- Select the
New Taxon Name
card from theHub
. This will lead to the first screen, where you provide the new name and its parent.
UCD Specific Note: UCD@TW has been previously populated with the data from John Noyes’ UCD, so inside the UCD@TW database you will not have to create a root
for the taxonomic name tree (that is, there should always be a parent taxon). First, fill out the name of the highest-level taxon that you are creating, and indicate its parent taxon. For example, if you are creating a new genus with 2 new species, first create the genus, and then create the two new species. If one of the two new species is type-species for the genus, you can come back to the genus name and add the type-species later.
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Note that TW is smart, and as soon as you enter the name, it checks to see if it already has it.
Next, select the
parent
. This should provide a list of possible parents, pick the correct one.- Based on the rank of the parent, TW will then ask you to select the
precise taxonomic rank of the new name
(see below). If everything is correct, hitCreate
. This will open up the next screen.
- Based on the rank of the parent, TW will then ask you to select the
Now you provide the
Source
(publication) andauthors
. If you have pinned the source, thepinboard
icon will be blue and you can click it to automatically fill in the source details.Then choose
Person
, and enter enough letters to bring up each author (they should be in the database if they were entered with the source).- If the authors of the Source are the same as the authors of the new name, you can click the button to the right
Clone from source
. - If multiple persons pop up that appear to be the same (for example
A. Dal Molin
andAna Dal Molin
), you can use theUniquify People task
to resolve and merge them (see Scenario: Resolving redundant person name strings, and matching author names with and without diacritical marks). - If an author name is not found, you can enter it and add it by clicking the green
Add New
button. This will add the author to the names table.
- If the authors of the Source are the same as the authors of the new name, you can click the button to the right
In most cases, for new taxa, you can skip over the
Status
andRelationship
fields. However, if the taxon is a fossil, you should checkFossil
in theStatus
field. he name will now appear with a little cross symbol to the left. There are special rules in ICZN and TW for fossil taxa.
The Type
form is next, which opens up a new form to capture details on the type. We prefer to complete the rest of the New Taxon Name
form first, and then do the Type
.
For new species, the
Original Combination
will be the same as used in the paper, soSet as Current
.Finally you can specify the gender and form of the new name. For species-level names there are four possibilities:
Adjective
. Most species epithets are probably treated as adjectives, for example, Signiphora flavella meaning a yellow species. These will change their ending if moved to a genus with a different gender. Names with the suffix “-ensis” (usually referring to a place), change the ending only if put in combination with a genus name that is neuter, in which case it becomes “-ense”.Noun in Apposition
. These don’t change gender when transferred to other genera with a different gender. An example might be a name like Aphelinus mali, named after the common host, the woolly apple aphid. An arbitrary combination of letters is treated as a noun.Noun in genitive case
. These are commonly patronyms, ending in “-i” for males and “-ae” for females.Participle
. A participle is an adjectival form of a verb. These are treated as adjectives, and they must agree in gender with the genus name.
There is a text field to capture the
Etymology
, in most cases you can simply paste this text from the publication.Be sure to
Save
all the information (greenSave
button at upper right) before moving to theType
screen. (UCD prefers to enterType
information last, after everything else on this page has been saved).
In most cases, the Quick type
screen will provide all the details you need to enter information on the type, and this is what we show below. However, if you have other information to add for the type, such as Lat/Long data, you will need to use the Comprehensive
form.
First, pick the nature of the
type
(for most new species this will be a holotype), provide thesource
(click bluepin
button if source is thedefault
), and thepage number
(s) on which the type is designated. The rest of the information on the type is filled in with the screen below.- In most cases, the type will be a new specimen, not already in TW as an
Existing Collection Object
. If so, clickNew
. - Paste the label data for the type into
Buffered Collecting
event. This is a verbatim text field. - In most cases, you can ignore
Buffered determinations
, andBuffered other labels
. - Total is number of specimens (one for a holotype).
- Designate the
preparation type
(pin, slide-mount, there are several choices). - The
Repository
is the institution where the type is deposited. Hopefully the repository will be in the TW table, otherwise you may need to create it using theRepositories card
in the Data portfolio. Collection Event
refers to a specimen already in the TW database, which in most cases will not be the case if you are curating a new species description.- In
Biocurations
, indicate whether the type is an adult or immature, and a male or female. - Finally, you enter the Identifier for the type, which consists of two parts. You must first Search for the
Namespace
(see the Glossary above) of the collection in which the type is deposited. Note that this may be different from the repository (a single institution may have several collections, each with a different “namespace”). Think of thenamespace
as the part of a specimen ID number that does not change for each specimen, for example,TAMU
inTAMU x01234567
. If the namespace is not in the database, you may need to create it, but since these are shared across projects, there is a good chance it will be there. Once you have selected the namespace, paste in the type or specimen number (only) in theIdentifier
field, and hit the greenCreate
button.
- In most cases, the type will be a new specimen, not already in TW as an
[INSERT SCREENSHOT]
If you wish to add paratypes
(optional), you essentially follow the same process for each one.
For many contemporary taxa, there may also be a ZooBank number
associated with the species. The correct way to enter this is to:
- Scroll to the top of the
Edit Type Specimen
page (orEdit taxon name
page) and click theRadial Annotator
to the right of the blue species name.- In this case, the
Identifier
will beGlobal
. - Pick
Lsid
, and enter theZooBank accession number
in theIdentifier
box. Note that some publications will provide the link to ZooBank which is not accepted by TW, but not the actual Lsid. In this case, navigate to ZooBank to get the valid Lsid, which will have the following format:
- In this case, the
urn:lsid:zoobank.org:act:5EB72879-1E9C-4A89-BCD8-FF37534B7172
If the paper does not list an Lsid for the new species, it might be worth a try to find it on the Zoobank.org web site.
- Be sure to click the green
Create
button at the bottom of the screen before leaving!
You show now add any additional information about the new species (or genus) in the publication following the process described next.
If you are creating a new genus-level
or family-level
name, the process is similar, but in many ways more simple because the type will be a species name or a genus name, respectively. If the type-species or type-genus name is also new, probably the easiest path would be to create the family-level or genus-level name first, then create the name of the type-species or type-genus, and then return to the new genus-level or family-level name and indicate the type. If you enter an existing name in the New Taxon Name
task and select it (assuming it is found), TW will take you to the Edit Taxon Name
screen where you can enter the type information.
After you click Create
and Save
you should be returned to the Browse Nomenclature
page:
[INSERT SCREENSHOT HERE]
If you have entered all the information correctly, it should be shown here. Note that the Validation
form can serve as a checklist. In this case, we have neglected to enter several items, indicated here. To fix these, the easiest way is hit the Navigate Radial
button (3 at upper right) and from here choose Edit
. We think the easiest way to proceed from here is to hit the Browse OTUs
button (1 at top of screen). This takes you to the summary form for the OTU that you have just created. Note that there is a similar icon on the Browse OTUs page, which will take you back to Browse Nomenclature
page. This is an easy way to move back and forth between these two important screens.
Add more species information
To add additional information about the species from the publication, first navigate to the OTU corresponding to the new taxon name. From the Browse nomenclature
page for the taxon, you can hit the Browse OTU
icon at the top of the page. This takes you to the OTU that is associated with the taxon:
Alternatively, you can use the Browse OTU
task to find the OTU. TW may bring up more than one choice:
[INSERT SCREENSHOT HERE]
In this case the OTU name with the check mark refers to the protonym (name as originally published. The OTU name followed by (c) refers to a subsequent combination. It is best to choose the subsequent combination as this will ensure that the data is tracked correctly.
(UCD-specific note: in this case, there is a third choice, which looks like a ghost, that is, a name that was created as a string when host or distribution records were imported from the original UCD@NHM. You should ignore ghosts. UCD@TW are working on eliminating them).
The most common tasks at this point will be to capture Citations
, Asserted Distributions
, and Biological Associations
.
Citations
. These provide a way to capture any information that is in the publication (e.g. whether it includes a diagnosis, whether the taxon is figured, information on hosts or distribution, etc.), andpage numbers
on which the information is found. Citing the exact page numbers will help subsequent users quickly find this information in long publications treating many species.- To enter this information, hit the
Radial Annotator
at top of screen - Choose
Citations
, enter the source (it should still be pinned) - Enter the exact
page number
s on which the information is found in the publication - Click
Create
- Click the blue
All
button for a list of currently used topics. Select the ones that are relevant - Scroll to the bottom of the screen, and click the green
Create
button. - When you close this screen (x at upper right) you should return to the OTU (
Browse Taxa
) page. If you refresh this in your browser, you should see thecitation
you have created in the upper right.
HINT: Topics
are unique to each project. For the UCD project, having created a lot of topics now, they suggest creating a new topic only if absolutely necessary.
For those working on other projects, you can use the Manage Controlled Vocabulary Terms
card in the Tasks portfolio to create and define new topics. Here, the Keyword
tab at the top refers to Tags
, discussed above, and the Topic
tab refers to Topics
.
Asserted Distributions
- Click the blue
Quick Forms
iconat top right, and follow the instructions to pick geographic areas from which the taxon is reported. This is the place to capture information from a
Distribution
section of the publication. - Enter the
source
which should still be pinned, and the exactpage numbers
on which the distribution information is given.Is Original
means this is the first time that this distribution has been published.Is absent
presumably means that the publication states that the taxon is not present in the designated area, but UCD notes they are not sure when to use this.
- Next, enter the most restrictive geographic area present in the TW database, which in most cases will be a state or a province.
HINT: If the paper contains many new asserted distributions, it is more efficient to record these using the New Asserted Distribution task
. Here you can lock in the source and each OTU, and enter the geographic areas one by one, without having to repeat the other information. In this example, we have locked the source and OTU (red arrows below), and we can enter geographic areas one by one. The task contains other tools (not shown below) that enable you to clone combinations of the Source/OTU, Source/Geographic area, or OTU/Geographic area.
[INSERT SCREENSHOT HERE]
Next, update the tags
(if necessary) to track progress. UCD Example, once you have entered the distribution
data from the source, if you are not at this time going to enter other information such as biological associations, add the Source processed – Distribution
tag to the source.
Biological Associations
. These are also accessed from the blueQuick forms
icon. The form is shown below. Examples presented here are UCD-based. You may have to enter more information as host data may or maynot already be in your instance of TW.
[INSERT SCREENSHOT HERE]
- Selecting
All
(1) will bring up a list of allBiological Association
in the project (2).
(UCD-specific note: In general for chalcidoids, you will want to capture the Primary (animal) host
or Plant host
, Plant Associate
in the case of parasitoids, or Parasitoid host in the case of hyperparasitoids).
- Pick the relevant blue tab and then hit the blue
Search
button (4) to find the host or associate name in the TW database. In most (UCD) cases, this will be a plant or animal name, so select OTU (3).- Search for the taxon name in the database (this brings up a select OTU search box). The UCD database is extensive, and usually the host will already be there, either as a
Taxon Name
or as anOTU
. If TW finds either of these, it will bring them up for you to choose. - If neither are found, TW will ask you if you want to "customize an OTU with that name". Say yes, and cut and paste the OTU name in the OTU box that comes up. Leave the Taxon Name box below the OTU box blank. IF YOU DO THIS, BE SURE YOU ARE SPELLING THE NAME CORRECTLY! For this reason it is best to cut and paste whenever possible. There is probably no reason to enter the author name of the OTU, but it doesn’t hurt anything.
- Search for the taxon name in the database (this brings up a select OTU search box). The UCD database is extensive, and usually the host will already be there, either as a
- Once you have entered the host or associate OTU, enter the
Citation
(source) (5) andpage number
(s) on which the information is located. - As above the
Is original
box (6) means that this biological association has not been published previously. So check this box if this is new information not published before. - Use the
Browse OTUs
page for the taxon (accessed with theBrowse OTUs card
) to see all previous biological associations recorded in TW for that entity.
At this time, there is no Biological Associations task comparable to the Asserted Distributions
task (this has been requested of the development team).
- IF you are entering several new
Biological Associations
from a paper, you can lock the citation for the source by hitting the little lock icon next to the pinboard icon in the Citation box. - [INSERT SCREEN SHOT for above]
Since most new species will be compared with other existing species, you will want to capture this information also. This is treated as another Biological Association, since any comparison will involve another OTU.
- Repeat the process for hosts, but choose
Compared With
(instead of associate) and follow the procedure above.
After completing these tasks, close the form and return to the OTU page for the taxon. If you refresh your browser, all the new information should be displayed.
[INSERT SCREEN SHOT of OTU for a taxon showing biological associations]
Remember to make good use of the tags
for tracking progress.
- If you have entered data for the biological associations reported in a paper, but are not planning to enter other data such as geographic distributions at this time, add the
Source processed – Biological Information
to the source. - If you have entered all nomenclatural acts in the paper, all relevant topics associated with the citation, all distribution information and all biological information, remove any tags associated with processing and add the tag
Source processed – Complete
to the source. Congratulations, you have successfully and completely curated this publication!
Enter information on an existing taxon
Before you do this, we recommend you add the Browse Taxa
and Browse Nomenclature
cards to your favorites for easy quick access.
- Check to ensure the publication source you are working with is on your
Pinboard
and selected as thedefault
. - Navigate to the taxon (OTU) using the
Browse Taxa card
in tasks - Once you have found the correct taxon, proceed exactly as instructed above for a new taxon.
HINT: There is at least one important caveat. If you are capturing information for a species that is currently used in a different combination from the genus in which it was originally described, you may get two OTUs for the species name when you search for it in Browse taxa
.
- one will be the
OTU
attached to theoriginal protonym
(indicated by acheck mark
next to the name) - one will be the
OTU
attached to thecombination
(indicated by ac
next to the name). - Use the OTU attached to the combination, at least for now. This is an area of the database that is still being worked on, but this should facilitate downstream display of the new information.
Add / amend type information for a new taxon
For many older species group names, there will be no information on the type in TW. If you wish to add this information, you will want to have the original description handy, and pin it to the Pinboard
. The easiest way to proceed is to use the New type specimen task
. You can then follow the steps above for designating a type for a new species.
HINT: The New type specimen task
is also used to add or modify information on types already in the system.
New synonymy or removal from synonymy (stat. rev.)
- Find the
junior synonym
name using theBrowse Nomenclature
task. - Click the
Edit
iconto navigate to the
Edit taxon name
page. - Enter the
senior synonym
in theRelationship
box. A list of candidate names will come up. - Select the correct one and Set to
Parent
.- A list of choices for the synonym relationship will include
Subjective synonym
,Objective synonym
,subsequent Misspelling
, andHomonym of
.
- A list of choices for the synonym relationship will include
- Note that you must also
tag
this nomenclatural act (new synonymy) to a citation and page number.- Click the
Radial Annotator
icon to the right in theRelationship box
, and chooseCitations
. - Enter the
Source
(use the blue pin key!) andpage number
(s). - If this is the first time the synonymy has been proposed, check the
Is Original
box.
- Click the
Transfer species to new parent or not
If the junior synonym is a genus name, you must then decide if you want to transfer some or all of the species to the new parent.
- Once you have made the synonymy, TW will present a table called
Manage Synonyms
. This shows the current parent, and by default, the new parent. You can change the latter to cover cases in which a genus is being split up and the species are being moved to different genera.- You can select species individually, or select All of them.
- At the bottom of the screen click the green
Move
button. TW will ask you if you are sure you want to do this!
HINT a la UCD@TW: It is the consenus of UCD@TW curators that if a genus is synonymized under another genus, and the author(s) of the paper do not explicitly treat generic placement of the species formerly contained in it, that all species are considered to belong to the senior synonym, by default.
Remove name from synonomy
- To do this, find the junior synonym and move to the
Edit taxon name
page as above. - Scroll down to
Status
and click theShow All
button to the right. This brings up a list of all possibilities. - Choose
Valid
(nested under Available), and then be sure to - enter the
Source citation
and pagination as above, but this time use theRadial annotator
in the right lower corner of theStatus
box.
New combination
In an older version of TW, your strategy depended upon whether the combination is really new (that is, the species has previously been placed in that genus), or whether the combination had been used before. Scenarios 1 and 2 below cover those cases, respectively. Both procedures still work, but as of November 2021, there is new functionality on the Edit Taxon Name
page that allows you to handle either case. This is shown as option 3 below. Option 3 is probably the easiest, most preferred way to handle all new combinations now.
For New Combinations.
- Open the
New Combination
task, and type in the new combination. TW will bring up a list of candidate genera and candidate species.- If you enter a trinomial (for assigning to a subgenus, TW will show 3 sets of names. Pick the correct
genus name
andspecies name
- Click the
pinboard
icon to paste in thecitation
, add thepage number
, and hitCreate
.
- If you enter a trinomial (for assigning to a subgenus, TW will show 3 sets of names. Pick the correct
- Once you have created the new combination, be sure to click the
green button
to move the species to the new genus.- (The only time you would not want to move the species to this genus is if you were entering a historical combination, and the species is not currently classified in that genus). It’s as simple as that!
Combinations used before.
- Navigate to the
Edit Taxon name
page for the species. - Change the parent to the current genus (the
revived combination
). - Then move to the
Radial annotator
to the right of the species name shown in blue at the top right of the screen.- Choose
citation
and enter thesource
andpage number
for the paper in which the former combination was revived.
- Choose
Option 3 (either use case above)
- Navigate to the
Edit Taxon Name
page for the species in its existing combination. - Change the
parent
to thegenus
in which it has now been placed. - Scroll down to the
Subsequent combination
box. ClickSet as current
, or drag down the old combination to the species line and enter the genus for the new combination on the genus line. - Enter the
source
andpage number
of the paper in which the transfer was published and clickCreate
.
The new combination
will be added to the chronological list at the bottom of the box, and it should show in the historical list when you return to the name in Browse Nomenclature
.
If the gender of species is incorrect following the new combination, you may need to change the Gender and form of the species name, and/or the gender of the genus (on the Edit taxon name
forms for the species name and genus respectively). This correction can also be made using Click to edit verbatim
(use sparingly).
Revised family placement for a genus or genus placement for a species
If someone has published a new family-level placement for a genus, recording this is a two step process.
- Navigate to the
Edit taxon name
form for the genus. - First, change the
Parent
at the top of theEdit taxon name
form to the newfamily-level taxon
.- If the family name has not been used at this hierarchical level before, you many need to create the
protonym
for it first.
- If the family name has not been used at this hierarchical level before, you many need to create the
- Second, you must record the
source
of this change. Scroll to the bottom of theEdit taxon name
screen and find theClassification
box. Search for the new family-level taxon andSet to Parent
. - In the
Radial annotator
that now appears, chooseCitation
and enter thesource
andpage number
where the revised placement was published.
If you are moving a subfamily, tribe or subtribe to a new family, the process is the same, but you would work from the Edit taxon name
screen for the appropriate family-level taxon.
To move a species to a different genus or subgenus, use the New Combination task Scenario . If you are moving a subfamily, tribe or subtribe to a different family level taxon, but the categorical level of the taxon you are moving does not change, follow the same procedure.
However, if you are changing the categorical level of a family-group name
, the process is more complicated, and you will need to refer to Scenario: Changing rank of a family-level taxon.
Designate nomen nudum or numen dubium
- To designate a name as a
_nomen nudum_
,_nomen dubium_
or asunavailable
, navigate to theStatus field
in theEdit Taxon Name
form.- The default for this field is valid. Four common choices are shown:
Unavailable
,Nomen Nudum
,Nomen Dubium
, andFossil
. - Click the
All
button here brings up a comprehensive list of other possibilities. For unavailable names you should probably look at the entire list and designate the reason the name is not available. - Be sure to enter the
source
andpage number
for the paper that published this information.
- The default for this field is valid. Four common choices are shown:
Homonyms and replacement names
The most common scenario will be that someone has discovered a junior homonym and provided a replacement name. Here are the steps you would follow. First be sure the source
is the default
in your pinboard
.
- First create the replacement name using the
New Taxon Name task
, as described above, entering all information on the authors, citation, etc. - Then move to the junior homonym (
Browse Nomenclature
, click the greenEdit
button at top right corner).- In the
Relationships
field, enter thesenior homonym
. - You will be given a list of choices, choose
Homonym of
.
- In the
- Now designate the replacement name. In the
Relationships
field, enter thereplacement name
.- HINT:
Replaced By
does not appear in the short list of choices, so either search for it (easiest) or find it in the table ofAll choices
. - Enter the
citation
andpage number
where thereplacement name
was published.
- HINT:
Resolving redundant person name strings, and matching author names with and without diacritical marks
Often when you enter a person's name string in a search field, such as for authors of a source or taxon, multiple entries will pop up that appear to be the same person, such as A. Dal Molin
and Ana Dal Molin
. The Uniquify People task
provides tools to resolve and merge these.
- Find one instance of the person in the
Select Person
field, and - Load another instance (probably with different abbreviations of names) in the
Match People
field. The task will show you information about each person, such as representative publications. - If you are sure that they are the same people, you can merge them by clicking the
Merge People
button.
Diacritical marks (e.g. umlauts, tildas) on author names pose special problems, as the search engines may not find them. For example, if the author name is Ferrière and you enter Ferriere (without the diacritical mark), the search engine will not find it. The best way to resolve this is to treat Ferriere as an alternate spelling
of the name Fèrriere. To accomplish this:
- Go to the
People data card
, and pull up the name. - In the
Radial annotator
at the top of the screen, chooseAlternate Values
- Then click the
Alternate Spelling
tab. - Select whether it is the first or last name, enter the alternate spelling, and click
Create
. Once this is done, the search engine will find the person using either spelling of the name.
Recording subsequent misspelling of a name
- First, you need to
create
the misspelled name using theNew Taxon Name task
. Do not give it an author. - Scroll down to the
Relationship
field - Search for the correctly spelled name
- Set the correctly spelled name as the
Parent
, and - Choose the
Misspelling Of
button. - Enter the
citation
(source) for themisspelled name
and thepage number
in theRadial Annotator
on the right of theRelationship
field.
Adding images to TW
Images can be attached to various entities in TW, such as Collection objects
(specimens) including types, OTUs
(concepts of taxa), Collecting events
, etc. If you put images in TW that are not your own property or are in the public domain, you should be sensitive to copyright issues. TW will accept images in PNG, TIFF, or JPEG formats. The following are probably the most common cases in which you might wish to upload images.
Type specimen images.
- Navigate to the
Collection object
form for the type using theNew type specimen task
, or go to theType
screen (eitherQuick
orComprehensive
) in theEdit taxon name
form. - If the type has not already been recorded (which will be the case for many old names), you will need to create it first. Drag and drop the image into the
Depiction field
(it contains the textDrop images here to add figures
), in either thequick
orcomprehensive type
screen.- Of course, if you do this, you need to be sure that the images are actually of the types! Note that you can add images to holotypes, allotypes, and all of the other types possible in the
Type
screen. - Note also that if you click in the box surrounded by a dashed line, TW will open a dialog box representing the folders on your computer where you can browse for the images.
- Of course, if you do this, you need to be sure that the images are actually of the types! Note that you can add images to holotypes, allotypes, and all of the other types possible in the
If the image is something other than the type specimen itself, such as labels of a type specimen label or a copy of notes on the type, then:
- Navigate to the
Expanded Edit
Radial navigator
to the upper right of theDepiction
field, - Choose
Depiction
and checkIs data depiction
. - If you are pulling the image from a publication, find
Citation
in theRadial annotator
below the image and give thesource
andpage number
.
OTUs.
Images illustrating taxa should be attached to OTUs
.
- Use the
Browse taxa
task to find theOTU
. - Note the
Radial Annotator
to the right of the name at the top left of the field has aDepiction slice
, which you can click on and then use to add the image. - Once the image has loaded, you can use the green
Edit
button to add afigure name
and acaption
. - If you are pulling the image from a published source, be sure to enter the
source
andpage number
, using theCitations
slice in theRadial annotator
to the right of the image. - To delete an image, click the red
trash icon
to the right of it.
Copyright issues.
To enter the copyright status
for an image, find the Attribution
slice in the Radial annotator
associated with it (it also has a copyright symbol in it). Here you will find a menu with different copyright options, the year of copyright, and various other places to enter the Creator
, Owner
, Editor
, and Copyright holder
for the image.
Associated with each image are a Label
field and a Caption
field. We recommend using the Caption
field only to record information associated with the image, such as "Fig. 2, male head, frontal view". The Label
field is intended for use primarily when using TW to create output such as species pages or publications.
It is also possible to batch process images using the New Image
task, which may be more efficient if you are uploading many images from the same publication. You can drag and drop batches of images, and then assign the author/creator, source (publication), copyright information and so forth for all of them at once. If you plan to attach the images to an OTU
or Collection Object
(including type specimens) upload only the relevant images in each batch. Then you can use the Depict Some
screen to assign them.
Changing rank of a family-level taxon
This is a multi-step process. You may need to raise or lower the rank of a family-level taxon. The process is the same. Here's an example: let’s assume that we wish to raise the categorical level of the taxon Coccophaginae to family level, Coccophagidae. Here are the steps to follow.
Check to see if Coccophagidae has been used at the family level before (use
Browse Nomenclature
). If it has, you can skip step 2 below, because the taxon name Coccophagidae already exists in the system.If the taxon at the family-level (Coccophagidae here) does not exist, navigate to the taxon name Coccophaginae (
Browse Nomenclature
) and move to theEdit Taxon Name screen
to create the name Coccophagidae.
- The best way to do this is to
Clone
the subfamily level name (green button in upper right), as this will retain the author and date, type genus, and other historical information. Select all the boxes
to retain all historical information and typeCLONE
in the box. This will active the greenClone
button. Note that you are creating ataxon name
here, not an OTU, which is a separate issue.
- You are now on the
Edit taxon name
page for the cloned name.
- Change the family ending suffix to “idae”, or Coccophagidae.
- Now change the parent. In this case, it will now be Chalcidoidea.
- Then
Show all ranks
, and pickFamily
.
- To record who made the change in categorical level:
- Scroll down to the
Classification field
- Click
Set to Parent
(which will pick up Chalcidoidea from above), if the current classification is correct. Otherwise, type in the correct parent.- Below the field will be two choices,
Incertae Sedis
andClassified As
. Pick SourceClassified As
.
- Below the field will be two choices,
- Enter the
source
andpage number
for the publication in which the change was made (in this case, elevation of Coccophaginae to Coccophagidae).
- Now you need to make the appropriate changes to the nominate subfamily taxon, the subfamily Coccophaginae in this example.
Navigate
to theEdit Taxon Name
form for Coccophaginae.- Change the
parent
here to the new family-level name, in this case, Coccophagidae.
- Next, scroll down to the Relationships field.
- Enter the new
family-level name
(Coccophagidae), and show all possible choices
(blue box to right).- Choose
Family Group Name, Original Form Of
from the menu of choices (it is belowUsage
which is belowUnavailable or Invalid, linked to
).
- Choose
- Enter the
source
andpage number
, as always.
At this point, a
Manage Synonymy
screen will appear. This provides a dashboard for assigning the classification of all taxa subordinate to the family name (children, in other words).Below the
Manage Synonymy
screen you will find theClassification
screen.
- Type in new
Parent
(Coccophagidae in this example), and - Choose
Source Classified As
. - Enter the
citation
andpage number
for the appropriate publication.
Changing rank of a genus-level taxon or species-level taxon
Example: to elevate a subgenus to genus level:
- First
Navigate
to the name of the subgenus and click on theEdit taxon name
tool. - Change the
parent
as appropriate (family, subfamily, tribe etc.) and - Change the
rank
to genus.
Next, how to record the citation? Note well, classification relationships should be used only above the genus level.
For making any changes in rank at the genus level and below use the New Combination task
: (explained in the New Combination Scenario
). There is still a 2-part process required at the moment.
- Create the combination (using the
New Combination
task), e.g. Camptoptera (Eofoersteria), and add thecitation
for same there. - Update the
classification
by changing theparent
for the "now" subgenus. You will be required to manuallyselect the rank
, (e.g. subgenus)
One should be aware that UCD@NHM did not use subgeneric names, they were treated as synonyms of the parent genus. However, if species names were originally described in a subgenus, the original combination was recorded and will show in UCD@TW as a combination, as in the following example:
INSERT Screenshot
If you are working with a genus in which a subgeneric classification has been used, you have the following options:
You can create all of the subgeneric names, or find them and treat them as valid children of the appropriate genus. Nominate subgeneric names can be created by cloning the genus name and changing rank (see examples for subfamilies above, section 4.14). Whether or not you want to take the time to do this is up to you and your colleagues, but the tools are there in UCD@TW and in TaxonWorks generally.
You can continue to treat the subgenera as junior synonyms of the parent genus. However, if you curate a paper in which a species is originally described in a subgenus, you should be sure to enter both the
Genus
andSubgenus
names in theOriginal Combination
andRank
section ofEdit Taxon Name
.If you want to record historic subgeneric placement, use the
New Combination task
.
Species groups
These are used in many genera of chalcidoids as informal grouping of species without nomenclatural rank or status. UCD@TW provides the tools to treat these formally (as superspecies which is what the ICZN recommends) but it will not display them as such in Browse Nomenclature
. However, the consensus in the UCD project seems to be that it is preferable to leave species groups as informal groupings without nomenclatural baggage. How then to indicate or record assignment to species groups? There are several options, each of which has strong and weak points. It is a "policy decision". You will have to decide which option works best for your group.
One.
- Add the
species group designation
to theOTU name
field using theedit OTU
function. The OTU can remain linked to the original taxonomic name. It will display as follows, every time the OTU name is displayed:
INSERT screenshot
Two.
You will need to use a data attribute with the Predicate name species group
and add the predicate as a default option to the OTU display.
- First, create a new
Predicate
using theManage Controlled Vocabulary task
. - Provide a
definition
and choose acolor
. - Next, go to
Project
(upper right corner of any screen) - Choose
Edit Preferences
underEdit
(upper left corner of screen) - Select
OTU
, scroll down toSpecies Group
and select it.
Now the Predicate
is created and will be available for any OTU
and can be designated where needed.
- Second,
Browse
to a particular OTU and chooseData Attributes
in theRadial annotator
. - Type
species group
in theSelect a Predicate
box, thename
of the species group in theValue
box, and click the greenCreate
button. - If you want to associate this placement with a literature citation, enter it using the
citations
button to the right of thespecies group name
at bottom of the screen.
Once you have completed Step One above, the Predicate
will be available for any OTU
, you can designate them using Step Two.
Three.
- Create a
Tag
for each species group inManage Controlled Vocabulary
, - Apply the tag to the OTU using the
Radial annotator
. This will allow you to pull up all OTUs assigned to a particular species group in theRadial annotator
. - Note well, however, the downside is that the tags will appear in the list for everyone in the project.
Four.
- Create a matrix of OTUs for each species group.
About tribes and subtribes
Again, using the UCD@NHM Project as an example, they did not formally recognize taxonomic levels between genera and subfamilies. Names of tribes and subtribes were treated as junior synonyms of their respective families. However, tribal and subtribal classifications are currently used in many families of chalcidoids. If you wish to incorporate these into classifications in UCD@TW, steps to follow are describe below. First, you must determine if the tribal or subtribal form of the name is in UCD@TW, treated as a synonym of the subfamily. See the entire scenario next.
One.
- To determine if the tribal or subtribal form of the name is in UCD@TW and treated as a synonym of the subfamily, go to
Browse Nomenclature
,search
for the name, for example,Coccophagini
.- Be sure that you do not have the redirect to valid name box checked!
- If you get a result showing the tribe (or subtribe) name in a black box to the right of the subfamily name (see below), the tribal form is in TW treated as a synonym of the subfamily.
In most cases, if the tribe or subtribe name has been used in the literature, it will show up as a synonym of the nominate subfamily. If it does not, you will need to create it, so skip to section Five below.
- Navigate to the name with the tribal name at right (not to the valid form of the subfamily name, which may come up without the tribe name in the black box). It will be shown as an invalid synonym of the subfamily.
- Click the green
Edit
icon to move to theEdit Taxon Name
form. Show all ranks
in theBasic Information
form and picktribe
.- Then change the suffix from
-inae
to-ini
and pick the appropriateparent
.
Two.
- Scroll down to
Status
,Show All
, and selectValid
. - Provide the
citation
andpage number
using theRadial annotator
to the right.
Three.
- If you wish to provide a citation for this usage of the name, scroll down to
Classification
, chooseSet to Parent
(in this case it would beCoccophagini
) - Choose
Source Classified As
.
Four.
- One more (obsure) task remains. Using the
Navigate Radial icon
to the right of the tribal name at the top of the page, choose
Show
- Then choose
Edit
in the menu bar at the top of the next screen. This takes you to an older version of theEdit Taxon Name
form. - If a name appears in the
Verbatim Name
field at the bottom of the screen (likeCoccophaginae ),
deleteit and click the green
Update Taxon Name` button. This removes an artifact created when tribal or subtribal names were imported as synonyms from TW@NHM.
Continue from this point only if the tribal or subtribal form of the name did not show up as synonym when you searched for it in step One above. Most likely, in this case it has not been used at this hierachical level before. If it does not show up, create it using the following process.
Five.
- Navigate to the taxon name at the subfamily level, for example, Coccophaginae (via
Browse Nomenclature
) and move to theEdit Taxon Name
screen. - Create the name at the tribal or subtribal level, for example, Coccophagini. The best way to do this is to
Clone
the subfamily level name (see green button in upper right), as this will retain the author and date, type genus, and other historical information.Select all the boxes
to retain all historical information and typeCLONE
in the box. This will active the greenClone
button. Note that you are creating a taxon name here, not an OTU, which is a separate issue.
Six.
- Navigate to the tribal (or subtribal) name in
Browse Nomenclature
and move to theEdit Taxon Name
screen. Pick
the rank (tribe) and change the ending to-ini
.- Change the
parent
. In this case, the parent of Coccophagini would be Coccophaginae.
Seven.
- Under Classification, set to parent (Coccophaginae) and choose
Source Classified As
. - Use the
Radial annotator
to the right to enter a citation for the publication and page number of the paper in which the tribe was recognized or moved.
Eight.
- The problem with this approach is that all of the children of Coccophaginae will have been transferred to Coccophagini. If some of these genera belong to another tribe, you will need to create any such tribe, using the steps above, and transfer the genera, one by one.
Taxon classified as Incertae Sedis
- First navigate to the appropriate taxon name
- Click the green
Edit Taxon Name
button. - Change the parent to the higher level taxon in which the taxon has been classified as Incertae Sedis.
- Navigate down to the
Classification
field - Click
Set to Parent
, and chooseIncertae Sedis
. - Then record the source and page number in which the classification was made using the
Radial annotator
to the right.
Species name endings changing due to movement to another genus, or correction by publication
For some name:
A - start (origin)
B - current -> current classification
change the parent here -> everything looks more or less right
C - second move
preserve "b"
A - Protonym
B - Combination
C - Parent (Combination)
From a practical standpoint, when a name changes, use New Combination
task. Why?
- It lets you create the new combination just by typing in the string
- Having that combination, even if its just a B, pre-adapts you for C's. This gives you the historical record.
- In the
New Combination
task, after the combination has been created, there is an option to easily move the name to the correct parent
Considerations vs. line endings.
- In the
New combination task
you will find/pick the species in its original latin form
- If that name has gendered data with it
- and the new genus has gendered data with it
- Then conjugation of the species name will automatically be rendered correctly in the new combination, and in reference to the new Parent (after you do 3) above)
- To pre-adapt your steps above being easy, follow best practices and add the gendered information at the time of entry of a Protonym.
- and the new genus has gendered data with it
Never just change parent, always go the Combination
route. (i.e. 2) above).
Example use case of name ending corrected by subsequent publication:
- Species published with incorrect ending
- Name is always the original form, latinized, never changed
- Author "corrects" the ending in a subsequent publication
- Key information: in this case there is no second Protonym, the gender ending correction happens automagically
- Key trick: to add a citation with this "fixed" data you must create a new
Combination
, and cite it. You must compose the combination with the same protonym that was "misspelled"
- Key bits of making new combinations
- Think about making your new combination by finding
Protonyms
in the original combination
- Remember if you type in a gendered ending, and no suggestions are found, you can always click to search directly by the original combination, or to track down the protonym in the taxon name autocomplete.
- For all of the above to work, the
Gender and form
section of theEdit Taxon Name
form on the original protonym must be filled in.
- Think about making your new combination by finding
Species synonymized with two or more other species
- A name is published.
- A type series is used (i.e. there is no holotype)
- The type series is found to represent two different species.
- The author says "we're stating this is two different species, and synonymizing the original name under two other names, but not selecting a holotype. If a future worker selects a holotype, our actions here may need to be changed again" (alternatively, author may synonymize the species in partim).
- Recommendation: Do nothing (do not post the two synonymies in TW) but add a citation and note, there are no governed consequences to manage.
- If you did have specimen catalog numbers then you could create 2 OTUs, each with the same species name, pre-adapting the data to receive new names for the new names if they come out.
- Recommendation 2: Use a
Nomen Dubium
status and attach a citation to this.
Junior synonym conserved by ICZN decision (i.e. senior synonym suppressed)
- Start at the
Edit Taxon Name
form for the suppressed name (senior homonym). - Under the
Relationship
section type in the suppressed name - And using the
Show all
button, selectsuppressed under
. - Cite this.
- Next, go to the
Edit Taxon Name
form for the junior homonym. - Under the
Status
section, use theShow all
button to findofficial list of specific names in zoology
and selectvalid
. - NB: use the
Advanced
button if for some reason theShow all
button is grayed out. - Cite this.
Entering names with incorrect endings for their taxonomic level
One method:
- Create name using correct ending,
Save
. - Designate as
Not Latin
under status. - Change the name ending to the form wanted,
Save
.
Second method:
- Create name. Using navigation radial, go to
Show
. - Click on
Edit
- Scroll down to bottom of form to
Verbatim
field and type in name as it was originally published. - Click
Update Taxon Name
Third method:
- Create the name. Click on
Edit
to get toEdit taxon name
form. - Click on
Clone
. - Select
Add invalid relationship
. - Type
clone
and then click theClone
button. Edit
theRelationship
field and selectFamily Group Name Form
.