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October 05, 2010

Incorporating species taxonomic data into Drupal

I've worked up a proof-of-concept that outlines one approach to incorporating species/presence information into the website. Here are the critical points:

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Looking at any taxonomic level (e.g., subclass Pterygota) shows four basic elements:
1) Descriptive text information (not present for most taxonomic classes but can be added later)
2) List of Taxonomic groups directly below the one being viewed
3) All species below this level in the tax structure
4) All pubs for taxa at lower levels

For example, here is the Pterygota subclass:
http://informationmanager.eeb.lsa.umich.edu/beta/taxonomy/term/11502

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Clicking on a species record gives you a bit more information. For example,
abagrotis anchocelioides:
http://informationmanager.eeb.lsa.umich.edu/beta/node/12021

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Finally, here's a point-blank list of the species I've imported:
http://informationmanager.eeb.lsa.umich.edu/beta/insect

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Notes:
1) Taxonomic information is not perfect (Proof of Concept only!!)
2) If we ever digitize the collections, this format should be extensible. I would probably add a "Specimen Record" content type to hold the Collector, Date, etc. information and have it reference the species.
3) This should also be extensible in that we could potentially the information stored with data from EOL, GBIF, TOL. Stuff like synonyms, descriptions, authorities...

Challenges:

1) Some of our presence records are only to the Genus or Family level, how to deal with these?
2) Getting all of the species lists into order! Standardizing the taxonomic hierarchy we use.
3) Creating connections from the publications to the Species Taxonomy list.

Technical Notes:
1) One Vocabulary (call it "UMBS Species Taxonomy") is used. It is hierarchical and includes the following taxa:
Kingdom > Phylum > Class > Subclass > Infraclass > Superorder > Order > Family > Genus. See below for species.

2) One Content Type (call it "Species") is used. It contains fields such as Species Name, Source, Species Presence (i.e., is it found at UMBS proper or in the Region?) and a Content Taxonomy field that references UMBS Species Taxonomy.

Note: I'm not 100% committed to Content Taxonomy. Pluses: Allows autocomplete without free tagging, reference to a vocabulary is just another cck field. Minuses: Yet another module, others?

3) Views + Panels are used to implement search and display.

Posted by kkwaiser at October 5, 2010 03:43 PM

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