Wiki modelling - Part 3

I rather skirted around the notion of "taxonomic concepts" in the previous post, partly because it's easy to end up with trying to have a concept for each utterance every made by a taxonomist, and that doesn't seem, er, scalable. So, I have a more limited view of a taxonomic concept, namely a name attached to some data. For example, I think the NCBI Taxonomy provides useful taxonomic concepts, in that names are explicitly linked to data, such as sequences:

Having data means we can make inferences that have some basis, other than trying to figure out what a taxonomist "meant".

However, things start to get a little messy once I try and extract more information out of NCBI GenBank. Some time ago I pointed out the potential utility of host association records in GenBank. In some (many?) cases the host taxa won't be in GenBank, so the link will be between DNA sequence and taxon name. This is, of course, a simplification. It would be nice to model things more accurately. For example, a parasite will typically be obtained from a host organism, so it might be nice if, say, we had voucher specimen codes for both parasite and host, and could model the link as one between organisms (or samples of/from organisms). However, this is unlikely to be feasible in most cases, hence we have sequences linked to names:

Wiki modelling - Part 2

Modelling taxa is a bit trickier. I've sketched my ideas for distinguishing name strings and taxonomic names earlier. That's the easy stuff. What about "taxonomic concepts" and "OTUs"? As a first pass, I'm looking at linking taxon names to classifications via GUIDs. If a taxon appears in a classification then the GUID of the corresponding node in the classification is an attribute of the taxon name, and each classification GUID (representing a node in a classification) corresponds to a page in the Wiki.



I claim no originality for this, it's very close to how uBio models classification concepts:



The trick here is going to be ensuring that I can do sensible queries, such as linking a node in a classification to alternative names.

The other entity that I need to think carefully about are OTUs (Operational Taxonomic Units). By OTUs I mean the taxa that appear in phylogenetic trees. In the TbMap project I mapped TreeBASE taxa to names in external databases, but noted that TreeBASE taxa are better thought of as OTUs:

...many taxon names in TreeBASE are best though of as Operational Taxonomy Units (OTUs) rather than taxonomic names. They identify a set of observations for a particular specimen, set of specimens, or a taxon. For instance, "Eleutherodactylus crassidigitus FMNH257676 Panama" (TaxonID T51971) refers to a 1200 base pair stretch of mitochondrial DNA (AY273113) obtained from Field Museum Natural History specimen FMNH 257676, which has been identified as Eleutherodactylus crassidigitus. [see doi:10.1186/1471-2105-8-158.

Taxa in phylogenetic trees may be single sequences, multiple sequences (from one or more specimens), or aggregates of information from multiple taxa. The challenge is to model these in the simplest way that reflects this, but also makes queries feasible. What I'm aiming for is for the user to click on a node in a phylogeny, and be taken to a page that best corresponds to the entity in the tree, but at the same time enable queries that will list all phylogenies that contain a given taxon.

Wiki modelling - Part 1

Time to make some notes. I've been playing with using Sematic Mediawiki to create a database of taxonomic names, literature, specimens, sequences, and phylogenies. One challenge is to come up with simple ways to model these entities, in a way that makes both data entry simple and querying as simple as possible. Some things are straightforward. For example, a publication can be modelled like this:

OK, I've ignored the attributes. The diagram simply shows the use of MediaWiki REDIRECT to enable the use of standard publication GUIDs as Wiki page names (see earlier posts for more details, and a hack to deal with problem characters in DOIs). One benefit of GUID REDIRECTs is that I can refer to publications using GUIDs, and the wiki user will be taken to the article page without any fuss.

Likewise, we can model a journal like this:

Again, GUIDs are REDIRECT pages. This means an article page can have the ISSN of the publication it appears in as one of its attributes, and we can then use ISSNs in our queries.

People are a bit trickier, given the absence of GUIDs (or the desire to keep obvious ones, such as email addresses, private) (see doi:10.1371/journal.pcbi.1000247 for some background). I plan to have a single page for each author, and have alternative spellings link to that page:



This is one motivation for my work on equivalent author names. By finding clusters of equivalent names it would be possible to pre-populate the wiki with author names from bibliographic databases, whilst minimising the number of duplicate pages for the same author.