Taxa page

Revision as of 14:59, 25 October 2012

Anatomy of the taxa page

The taxa page is essentially the hub of a species file website application. On the taxa page (Taxa hierarchy as it is formally called), a user may navigate up and down the taxonomic hierarchy via hyperlinks, view detailed information associated with the “current taxon,” and modify how the information is displayed. This section will briefly outline the main navigation features as well as the various data items that can be associated with the current taxon. The discussion will follow in the order of appearance of the various items on the taxa page. How some of the information is displayed and what options are available depend on the user’s log-in privileges. Finally, the options for changing what information is displayed will be discussed.

Insert new image (Taxa page from Orthoptera)

Insert image (Taxa hierarchy) Figure 1: Orthoptera as the current taxon

Understanding the importance of the current taxon is key to navigating through the taxonomic hierarchy and recognizing the different types of taxonomic data associated with a particular taxon. The current taxon (Orthoptera in the above image) is the one that is displayed when Taxa is clicked on the navigation bar. Upon entry to a new species file, clicking Taxa for the first time will display the taxon data for the apex taxon (the taxon at the top of the hierarchy for that species file). After navigating up or down the hierarchy, the last taxon displayed on the taxa page remains the current taxon. If one of the other menu items on the navigation bar is selected, a subsequent selection of Taxa will return to the previous current taxon display.

Navigate to current taxon’s parents

In Figure 1, Orthoptera is not only the current taxon but it is the apex taxon of the Orthoptera Species File as well. Superorder Orthopterida is the parent taxon, cohort Polyneoptera is the grandparent taxon, and infraclass Neoptera is the great grandparent taxon. Clicking one of these hyperlinks will select that taxon as the new current taxon.

Please note when navigating to the upper levels of a species file, selecting one of the above hyperlinks may transport the user to a different species file. In the image above, for example, selecting cohort Polyneoptera takes one to the Polyneoptera Species File and selecting infraclass Neoptera takes one to the Arthropoda Species File. This feature of automatic links is optional, but it demonstrates the possibility of seamless navigation throughout all species files.

Data items associated with the current taxon

There are many kinds of data that may be associated with the current taxon; some may be simple nomenclatural descriptions or commentary while others may be rather complex objects such as specimen or distribution data. It is rare for a single taxon to have all such associated data, but it is possible.

Nomenclatural details

The current status of the taxon is documented by its nomenclatural details. The species file software maintains a table of related taxa based on nomenclatural status. If a related taxon has been specified, it will be displayed along with the nomenclatural information of the current taxon.

If the current taxon is a secondary homonym (for example, use synonym Pezotettixschmidti Brunner von Wattenwyl, 1861), the nomenclatural details include: “Secondary homonym (Nomennovum is fieberi), Notschmidti of Fieber.” This example shows that multiple nomenclatural details may be included.

The following table contains nomenclatural information in several categories and parenthetically displays the kind of taxon relationship that may be specified.

Junior homonym Preoccupied (Nomen novum) Primary (Nomen novum) Secondary (Nomen novum) Unspecified (Nomen novum) Emandation Required (Incorrect original spelling) Unjustified (Correct spelling) Corrected lapsus (Lapsus calami) Unavailable Subsequent misspelling (Correct spelling) Incorrect original spelling (Correct spelling) Unnecessary replacement (Unnecessarily replaced name) Nomen nudum Suppressed by ruling Lapsus calami (Corrected lapsus) Misapplied Unnamed Unavailable, other reason (should be specified in nomenclatural comment) Other Junior synonym Incertae sedis Nomen dubium Nomen oblitum (Nomen protectum) Nomen novum (Junior homonym) Nomen protectum (Nomen oblitum) For family-group names based on same genus Original name Subsequent name Other comment (should be specified in nomenclatural comment) Nomenclatural comment (400 characters) Not [this taxon name] of (200 characters)

Table 1: Nomenclatural information Common names One or more common names may be associated with a scientific name. Not only can there be several names, editors who input the taxon data may create common names in different languages. An editor may add as many different languages as necessary. The set of languages varies from one species file to another.

Figure 2: Example of several common names In the above example from the Orthoptera Species File, subfamily Meconematinae has four common names, three of which are in English, and one is in German. Images

Any type of image may be associated with a particular taxon. An image can be a photo, line drawing, even a replica of a specimen label .

Figure 3: Minimum number of images displayed on taxa page There are 14 images associated with the species Extatosomatiaratum in the Phasmida Species File. The default setting of images on the taxa page displays only six images. The order in which the images are displayed is determined by the person who entered the image data. Clicking on the “See all images” hyperlink displays all of the images associated with this taxon.

Figure 4: Expanded image display In this expanded image display, there are three rows of images. The hyperlink “specimen” appears after all images associated with a specific specimen record. Hovering over the “specimen” hyperlink displays the specimen ID. [I guess we’re not hiding all IDs for the public user.] The hyperlinks allow the user to access the specimen data directly.

• • • [hyperlink to Data for specimen display]

The maximum number of images per row is six. There may be taxa with seven or more images associated with the same specimen record. In this case, the hyperlink “specimen” appears after each row of images but will go to the same specimen data display. Note the last four images are not associated with a specimen.

Clicking the first thumbnail in the second row displays a larger image and includes several options:

Figure 5: Single image display Please note: The single image display of an image not associated with a specimen does not include the hyperlinks for “Show all images for this specimen” and “Show specimen data.” This image (Figure 5) is actually the holotype of a synonym of Extatosoma tiaratum. [*** hyperlink to discussion of synonyms in specimen section]

To see the image displayed at its maximum resolution, click on the “See full size” button. The image below shows a magnified slice of Figure 5:

Figure 6: Full resolution detail of synonym of Extatosoma tiaratum Several images may be compared side by side. Click on the “Explain” hyperlink (seen in Figure 5) to see an explanation of how image compare works:

Figure 7: How to compare images In the following figure, there are three images selected for comparison: Two from Extatosoma tiaratum (one is actually the lectotype of a synonym) and one from Extatosoma popa.

Figure 8: Comparison of three images The user may select different resolutions and orientations for a close side by side comparison of any two images by clicking on the boxes below each selected image:

Figure 9: Side by side comparison of two species in genus Extatosoma The three hyperlinks at the bottom of the single image display (Figure 5) allow the user to • Show all images for this taxon: Displays all images, including those of synonyms. • Show all images for this specimen: Displays all images associated with the same specimen. This option is not displayed if the selected image is not associated with a specimen record. • Show specimen data: Displays the data for the specimen record. [hyperlink to Specimen data display]

Sounds

Sound recordings may also be associated with a particular taxon. This is particularly useful for the study of taxa whose calls or songs distinguish one species from another. Audio data was particularly important for the Orthoptera Species File, the first species file developed .

Figure 10: Orthopteran species with common name, images, and sound recordings Clicking the first sound icon, male from Durhan, CT, USA, to see (and hear) the associated recording:

Figure 11: Sound player options: Defaults are instant play and WAV format for PC By default, instant play is on which means the sound is automatically played upon first entry to the sound player. Instant play can be turned off; the last setting stays in effect for the remainder of the browser session. The default sound file format is WAV for the PC. The user can select AIFF format for the Mac:

Figure 12: AIFF file format for the Mac To listen in MP3 format for either the PC or Mac, the user must click on the “Download” link. Here the user has a choice of opening the computer’s default media player directly or saving it as a file. The file names are listed with the appropriate file extension. Saving the audio segment to any of the file formats allows the user to do wave form analysis, provide a visual spectrogram or oscillogram, or edit sound segments. Note that certain sound segments may not be available in all file formats. An image may also be associated with an audio recording:

Figure 13: Sound recording with associated image Clicking on the image thumbnail causes a new browser window to open displaying the image. In this case the image contains a visual representation of the sound recording:

Figure 14: Display of an image associated with a sound recording [FIX TYPO ON LINE]

Links

One or more links to other websites can be associated with the current taxon.

Figure 15: Links to other websites In this case, Alloperlaroberti (from the Plecoptera Species File) has links to two websites: The first is to an entomological site at Harvard and the second is to the IUCN list of threatened species. Clicking either link opens a new browser window and displays a web page pertaining to Alloperlaroberti.

Supplementary information

[For purposes of discussion, the image of the taxa page for Stilpnochloraacanthonotum will be used as an example for the next several sections.]

Figure 16: Taxon page example for supplementary information, distribution, scrutiny, and type information There are three records of supplementary information for Stilpnochloraacanthonotum. Since a taxon may have any number of supplementary information records, separating the data into discrete records with a descriptive title is quite useful. Clicking on Etymology displays the following supplementary information.

Figure 17: Supplementary information content There are three records of supplementary information for Stilpnochlora acanthonotum. Since a taxon may have any number of supplementary information records, separating the data into discrete records with a descriptive title is quite useful. Clicking on Etymology displays the following supplementary information.

The bold headings Content, Source of information, and Date last modified are part of the supplementary information template.

Distribution

Distribution data displayed in map form can be represented in two different manners depending on what kind of data there is: Shade maps and Google maps. Maps do not contain data for invalid or extinct taxa. Maps of higher level taxa, e.g., genus rank, aggregate the distribution data of its subordinate taxa.

Figure 18: Shaded distribution map

Shaded maps: These maps include distinct shading for TDWG geographical levels 1 through 3. Origin of the distribution data is threefold: Specimen data that include the TDWG classification, references that specify locality data, and manual entry. Determination of the completeness of the data is also included. The following partial display shows a drop down list to select one reference that contains distribution data.

Figure 19: Distribution by reference Since distribution for a single taxon can be from multiple sources, including multiple references, showing the distribution based on a single reference may be useful.

Google maps: A Google map application shows points on a map based on latitude and longitude contained in specimen data.

Figure 20: Google map showing specimen distribution These maps become very useful when looking at genus or above as in the map for tribe Steirodontini:

Figure 21: Google map showing distribution for tribe Steirodontini

The legend contains multiple specimen locality data. The standard features of Google maps is fully implemented in the species file web application.