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The Future of Informatics in Digital Literature – or Literature
and it’s (Digital) Future
Donat Agosti and Terrance CatapanoPlazi
TDWG, Woods Hole, September 28, 2010
Literature, the tool to formalize our knowledge, and make it
part of the global knowledgebase.
< 15% of taxonomists opt for Open Access
Source: Zootaxa, publisher of ca 15% of all new taxonomic names
“The current scholarly communication system is
nothing but a scanned copy of the paper based system.”
Van de Sompel & Lagoze, 2009, The Forth Paradigm.
E.g. BHL‘s emphasis on scanning and images of text…
E.g. BHL‘s emphasis on scanning and images of text…
… and little efforts (by third parties) to provide better
access
„An articulated semantic structure facilitates simpler algorithms acting on World Wide Web text and data
and is more feasible in the near term than building a layer of complex
artificial intelligence to interpret free-form human ideas using some
probabilistic approach.“
Ginsparg, 2009, The Forth Paradigm.
Quantity vs precission
Howard Ratner, Nature: Nature on Mobile: http://river-valley.tv/conferences/stm-innovations-seminar-2009
A semantically enhanced, linked XML document based on
clean OCR
TaxonX
Text XML document
<tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="193329"/> <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie </tax:name> <tax:status>n. sp.</tax:status> Fig 1 D - F </tax:nomenclature> <tax:div type="description"> <tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 93, SL 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving to a sharp apical tooth, the apex parallel to the anterior clypeal margin. (Holotype with material in mandibles, so mandibles and anterior clypeus $ described below from paratypes.) Median clypeus....</treatment>
Treatment
Treatment≠©
- Get LSID from Hymenoptera Name Server for names; ZooBank?-Add new names
- Get bibliographic Metadata from HNS (MODS)
- Get bibliographic Guids from bioguid (or EDIT?)
- Get geographic long/lat from geonames.org
Plazi workflow: GoldenGate mark up as an example
-Get Guids for - CBOL- NCBI- specimen- images- .....
Plazi Search and Retrieval Server: Access to data
TAPIR, SPM
You
You
You
human
machine
Materials examined from literature in GBIF
Facebook tool to mark
up legacy publications
Mark-up comes at an (exorbitant) cost…
Mark-up comes at an (exorbitant) cost, if done at the
wrong time
Shift from legacy to prospective publishing
Taxpub NLM DTD
Taxpub NLM DTD:a collaboration between
National Library of MedicineZookeys
Plazi
Taxpub NLM DTD: taxonomic domain specific
extension of the NLM Publishing and Archiving DTD
NLM DTD
Taxpub DTD
Taxpub/NLM DTD+ production worklow
Zookeys
Taxpub/NLM DTD+ production worklow
Zookeys
XMLPrint PDF HTML Other Sites
External resources
Treatment + external links
Treatment + external links:GUID / LSID
Now that we will have LSIDs in your content in PMC, I was looking for an LSID resolver so that we can build links to all of
this content.
But, the only place that I was able to resolve your LSIDs was on your zoobank.org/?lsid= service. I could not resolve them on
lsid.tdwg.org or bioguid.info/lsid.php. Perhaps I don’t understand how LSIDs are supposed to work, but I thought that
any LSID resolver should be able to resolve them. If only your local resolver resolves them, then are they really LSIDs or are
they just zoobank IDs dressed up like LSIDs?
Email from Jeff Beck, NCBI
Why do we do all that?
Technically, we are far beyond the doable
Technically, we are far beyond the doable, we need your
input:Why do you want to have a
(taxonomic) publication?
Why do you want to have a (taxonomic) publication?
External links?Materials Citations?
Descriptions?Credit?
Where is your data so that it can be linked? How will it be
be standardized?
