Saturday, July 08, 2006

Disconnected databases

One consequence of having multiple databases is that they can get out of sync, that is, information in one database might not be updated to reflect changes in another. I've touched on this earlier when discussing unidentified ants in GenBank (Discovering new things and Ants, RDF, and triple stores).

I've also come across cases where AntWeb is out of date. For example, the ant Strumigenys rubigus was described in 2000 by Brian Fisher. In the TaxonX marked up version of the original paper (available here), the holotype is listed as:

Holotype worker, Madagascar: Prov. Toamasina, F.C. Andrianantantely, 18 deg. 41.7 min. S, 48 deg. 48.8 min. E, 530 m 4-10.xii.1998, ex rotten log, rainforest, #49-2 (H.J. Ratsirarson) (MCZ).

Now, in an ideal, joined-up world, we'd have a link from the Fisher paper to the actual specimen. A bit of fussing (i.e., searching for "Strumigenys rubigus" on AntWeb) reveals that the holotype is casent0005630. The AntWeb page for this ant has no indication that this is the holotype, although there is a picture of the specimen labels that make it clear that this is what it is.

Having multiple sources of information makes it harder to keep things up to date, which is another reason why I think RDF and triple stores (or distributed queries) will help. So long as we have metadata about the specimen and the publication, we can make the inference that casent0005630 is the holotype of Strumigenys rubigus. This may ease the burden on individual databases. Rather than the curators of AntWeb having to update AntWeb manually every time a new name is published, a portal along the lines of my SemAnt toy could summarise this new information easily, if (and it's a big if) we have the links between publication and specimen.


  • I've always empasized that the 'true' value of data cannot be fully realised unless it can be linked to 'context' (related) data from multiple sources.

    Data costs a lot of collect, format and manage. Therefore make the most out of it (and riase your profile) by ensure its ability to interconnect.

    Such useful examples highlight the devaluation of the potential of data.

    By Blogger Lee, at 12:54 am  

  • Here is the treatment of rubigus

    < tax:treatment>
    < tax:nomenclature>
    < tax:name>Strumigenys rubigus< /tax:name>
    < tax:author>Fisher< /tax:author>
    < tax:status>sp. n.< /tax:status>
    < /tax:nomenclature>
    < tax:div type="description">
    < tax:p>
    HOLOTYPE WORKER. TL 2.9, HL 0.63, HW 0.48, CI 76, ML 0.32, MI 50, SL 0.40, SI 83, PW 0.34, AL 0.71. Characters of scotti-complex. Mandibles in full face view with outer margins shallowly and evenly convex, the width of the blade gradually decreasing from near the base to the apical teeth. Apical fork of each mandible of 2 stout spiniform teeth; without intercalary teeth or denticles between apical fork teeth. Each mandible blade with 2 preapical spiniform teeth, the proximal longer and slightly stouter than the distal, both teeth within the apical third of the length of the blade. Upper scrobe margin evenly and shallowly convex in full-face view, not bordered by a rim or flange, the eyes visible. Maximum width of eye slightly smaller than maximum width of antennal scape, 3-4 ommatidia in longest row. Antennal scapes short, stout, shallowly and gently curved and with their leading edges equipped with an apically directed row of spatulate or spoon-shaped hairs. Cephalic dorsum densely clothed with curved narrow spatulate to spoon-shaped ground-pilosity, the upper scrobe margin fringed with hairs which are the same shape and size as those on the dorsum. Dorsum of head reticulate-punctate. Pronotal humerus with a fine flagellate hair (absent on left humerus of type). Mesonotum with 1 pair of erect clavate hairs, located at anterior margin; shorter hairs which are curved toward the midline present posterior to this pair. Propodeum with 2 pairs of short, fine, posteriorly curved hairs immediately anterior of propodeal spines. Dorsal alitrunk with ground-pilosity as on head. Dorsum of alitrunk in outline very shallowly convex anteriorly and more or less flat posteriorly; posterior portion of mesonotum only slightly depressed below the anterior margin of propodeum. Humeral angles rounded. Anterior mesonotum without a carina above mesothoracic spiracle. Propodeal tooth broadly triangular, spongiform, lamellate, pointed apically, and subtended by a moderate infradental lamella. Alitrunk dorsum, and petiole densely reticulate-punctate. Side of alitrunk mostly with punctate sculpture, except for katepisternum which is smooth and shiny. Postpetiole smooth and shining. Spongiform appendages of pedicel segments moderately developed. In profile the petiole with a straight ventral strip that is slightly less in width than maximum width of eye. Postpetiole with moderately developed ventral spongiform lobes. Basigastral costulae arising on each side of a narrow, central clear area, remainder of gaster smooth and shiny. Dorsal surfaces of petiole, postpetiole and gaster with standing clavate to remiform hairs. First gastral sternite, including anterior half, with numerous short suberect filiform hairs. Colour light brown.
    < /tax:p>
    < /tax:div>
    < tax:div type="materials_examined">
    < tax:p>< tax:collection_event>
    Holotype worker, Madagascar: Prov. Toamasina, F.C. Andrianantantely, 18 deg. 41.7 min. S, 48 deg. 48.8 min. E, 530 m 4-10.xii.1998, ex rotten log, rainforest, #49-2 (H.J. Ratsirarson) (MCZ).< /tax:collection_event>
    < /tax:p>
    < /tax:div>
    < tax:div type="diagnosis">
    < tax:p>
    S. rubigus is distinguished from other species in the scotti-complex with the dorsum of petiole node reticulate-punctate by having the following combination of characters:
    < /tax:p>
    < tax:p>
    1) Mesonotum with only a single pair of erect hairs, located at anterior margin; shorter decumbent hairs may be present posterior to this pair.
    < /tax:p>
    < tax:p>
    2) In full-face view hairs on upper scrobe margin decumbent and sharply bent at basal third, not projecting well beyond the scrobe margin.
    < /tax:p>
    < tax:p>
    3) Anterior half of first gastral sternite with numerous short suberect hairs.
    < /tax:p>
    < /tax:div>
    < /tax:treatment>

    In the mark up process, you would then suggest to add within the tag

    < tax:collection_event>
    Holotype worker, Madagascar: Prov. Toamasina, F.C. Andrianantantely, 18 deg. 41.7 min. S, 48 deg. 48.8 min. E, 530 m 4-10.xii.1998, ex rotten log, rainforest, #49-2 (H.J. Ratsirarson) (MCZ).< /tax:collection_event>

    something like a LSID for this specimen, such as referring to the original specimen "casent0005630".

    This seems to be easily doable for the prospective publishing, but it might be useful already now to at least tag all the type material we come across processing legacy data and going through collections?

    By Blogger Donat Agosti, at 12:50 pm  

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