The Future of Informatics in Digital Literature – or Literature and it’s (Digital) Future Donat Agosti and Terrance Catapano Plazi TDWG, Woods Hole, September.

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?

http://plazi.org

Thank you very much!

Donat Agosti and Terrance Catapano

[email protected]