Thursday, February 28, 2008

TaxonConcept's Taxon Concepts II

Well, it is done ;) Here is an example which shows how our TCS XML looks like:

TCS seems to be really the XML standard to describe TaxonConcepts synonymy list entries.
The only open problem is how fine the granularity of a data set should be. I have now included any synonymy list of a distinct taxon in one TCS file. So our TCS granularity is at the taxon level. A finer granularity at he synonymy list level however also seems to be reasonable.

Wednesday, February 20, 2008

Dublin Core for Taxa

I recently wrote here that TaxonConcept will soon offer its metadata in TCS (Taxon Concept Schema) format to improve data exchange and interoperability with other groups. As the planned exchange interface will be a Open Archives (OAI) provider, we also have to deliver our data in Dublin Core (DC) format.
This brought up the problem how taxonomic data should be encoded in DC, which is mainly designed for document, electronic ressources and similar entities.
I had a short discussion with some of the members of the TDWG GUID list and decided to treat taxa similar to museum objects. For physical objects DC fields creator and date should contain e.g.the artist's name and date of creation instead of the name of the creator and publishing date of the electronic metadata representation. Therefore, I decided to use the creator tag for the taxon author, the date field as the date of description of the taxon and the title field for the taxon name. To describe the classification of a taxon I'll use the subject tag. Further, the relation tag will be used to handle the information TaxonConcepts stores from published synonymy lists.
An example:

<oai_dc:dc xsi:schemaLocation="">
Licensed under a Creative Commons Attribution 2.5 License
<dc:type>Taxon Concept</dc:type>
<dc:title>Eoglobigerina edita</dc:title>
<dc:creator>Subbotina, N.N.</dc:creator>
<dc:relation>Globigerina edita Subbotina 1953</dc:relation>
<dc:relation>Globorotalia (Globorotalia) edita Subbotina 1953</dc:relation>
<dc:relation>Eoglobigerina edita edita Subbotina 1953</dc:relation>
<dc:relation>Globigerina edita var. polycamera Khalilov 1956</dc:relation>
<dc:relation>Eoglobigerina edita polycamera Khalilov 1956</dc:relation>
Globigerina (Eoglobigerina) hemisphaerica Morozova 1961
Globigerina (Eoglobigerina) tetragona Morozova 1961
Globigerina (Eoglobigerina) pentagona Morozova 1961
Globigerina (Eoglobigerina) theodosica Morozova 1961
<dc:relation>Globanomalina pentagona Morozova 1961</dc:relation>
<dc:subject>Eoglobigerina edita</dc:subject>
<dc:subject>Acarinina nitida</dc:subject>

Friday, February 15, 2008

CHRONOS quo vadis?

Yesterday I found this interesting entry in the CHRONOS mailing list archive:
It seems as if CHRONOS has reached a very precarious situation, Cinzia has resigned and her letter speaks for itself..

Paleontology – The very late adaptors?

Even though one would think that the systematic nature of paleontology would lend itself well to computer-based approaches, the paleo community has been surprisingly slow to accept these new tools into their mainstream approaches. In the past years, from the perspective of science funding agencies, paleontology and taxonomy were not considered to be "sexy hot issues". Application of paleontology to climate research was fine, but systematic biology was "old school". The fragmentation of the community did not help its cause.

In fact, the closed-shop mentality of some groups has lead to the demise of promising, well funded projects, which were subsequently axed by the funding organisations. These projects had suffocated from their own arrogance.

Is there a lesson to be learnt? Science funders go a lot by what the scientific community wants. And maybe, in the context of web-based stuff, the emphasis should be on service – not on authority.

Surrender to the geographers? Never!

A few days ago at GFZ Potsdam we discussed whether we should continue fighting for the power of defining the term "geoinformatics" or whether we should leave the term for the geographers to play with and adopt something new. We decided to keep the term ... for now.

I remember distinctly from varsity in the 1990ies when someone suggested that we would need something like "biogeochemistry". This sounded really over the top at a time when "geochemistry" was already as interdisciplinary as one could go.

The time for "biogeoinformatics" will come, but for now I refuse to surrender the term "geoinformatics" to the geographers.

Friday, February 1, 2008

Surrender! Geoinformatics is GIS and we do 'biogeoinformatics'

Most people associate the term geoinformatics with geospatial information systems (GIS). Encyclopedia Brittanica online links the term with an article about geographic information systems. The Wikipedia entry for geoinformatics - despite giving a quite broad definition in the first sentence- also suggests this in it's definiton for the term.
But of course the term geoinformatics has a much broader scope, in my opinion it is covering any aspect of informatics in earth sciences. However, as the term was first adopted by geographers for geospatial info systems decades ago, geoinformatics will probably always remain (sniff..) .. GIS and remote sensing stuff.
In this light, is geoinformatics really the kind of science we actually are doing at Snet? Probably not. During the last years we have organized conference sessions which we called something like 'geoinformatics for sedimentology, stratigraphy and paleontology'. Yes, we indeed had some problems to correctly label our field of interest.
Today I found this page about biogeoinformatics of hexacorals and I thought: ..halleluja.. this is exactly what we are doing: bio-geo-informatics! Normally I hate these combinations of paleo-, bio-, geo-, chem-, phys- like paleobiochemical cycles of bla bla, but hey, we indeed do a bit of 'bio' and a bit of 'geo' and a bit of informatics, Bingo!
So I decided to surrender! I confess we are not doing geoinformatics, we are doing geobioinformatics, sorry: biogeoinformatics.