Setting the Scene for ViBRANT – Strategy, Philosophy and Communication

The Future of Scientific Publishing Donat Agosti (Plazi, Bern) 21 January 2011 Paris

I don‘t know the future, but I have a dream…

Immersing in the knowledge

I want to ask a publication a question, not the author telling me what I have to read.

I want to find out how many and which species are there? how are they related? do they disappear? how are they distributed?

I want to find out how many and which species there are how are they related do they disappear Other people have different interests

An example from the Neurocommons text mining pilot:
PubMed abstracts: > 16,000,000
CNS classified abstracts: 874,727
text mining recognized: 368,688
text mining processed: 94,381
extracted graph of 30,000+ relationships and 5,500 genes and proteins
“ protein-protein interaction networks” John Wilbanks, Neurocommons

In a semantic Web environment (where machines talk to each other and do most of our work), data need to be able to talk to each other: “ protein-protein interaction networks” John Wilbanks, Neurocommons 27,266 papers 4,563 papers 41,985 papers 10,365 papers 128,437 papers

It will open up scientific literature for data mining “ protein-protein interaction networks” John Wilbanks, Neurocommons

An example from the taxonomy text mining pilot:
Every year: > 17,000 new species described / year
Every year: >100,000 species redescribed /year
Total journals: >2,000 with taxonomic content
Total: 1,900,000 species described
Total: >20,000,000 treatments
text mining processed: 0
extracted graph of 0 species 0 relationships
Taxon mining project

1996 Conservation, Phylogeny, Systematics, Curiosity, Aesthetics, Fascination

2011 Experience, Frustration, Wonder, Excitment, Satisfaction, Determination

Modeling taxonomic literature: TaxonX Taxpub NLM DTD Plazi

- 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
.....

The semantically enhanced treatments, extracted, stored on Plazi.org, and served in a human readable form, are linked to the underlying data: Fisher & Smith, 2008, PLoS ONE.

Plazi Search and Retrieval Server: Access to data TAPIR, SPM You You You human machine

The conversion comes at a cost, even though GoldenGate and other editors exist

Time per minute to produce clean OCR using ABBYY; publications in chronological order Production metrics to measure effort and compare various approaches and alogrithm

How to mark up large body of legacy publications? Inhouse? Build / use commercial services? Use the community, e.g. volunteers? Activation energy Gutenberg Semantic Web Cost per knowledge

Training and demos...

Avoid it

Prospective publications: Zookeys / Phytokeys

Semantic enhancements to published texts

2036 ?

Why do we publish?

Public funded research

Contribute to the welfare of the nations…

Dissemination

Access

Before antbase.org, Harvard‘s Museum of Comparative Zoology could claim to be the only location with a complete set of ant systematics publications from 1758 - present. Through antbase.org‘s digital library, access to this body of literature is worldwide, and it is actively used (>10,000 visits in one month only).

Access to ant taxonomic publications through antbase.org /Smithsonian Institution, including currently the entire body of non-copyrighted publications since 1758 (>4,000 publications or 85,000 pages)

The Biodiversity Heritage Library is currently digitizing and make accessible >100 million pages, most of them out of copyright, ie older then 1925. ........ to be finished in 2048...

What is a publication from public funded science?

Open Access

What is a scientific publication? Print, journal, article, treatment, public funding, pdf, xml Tool to disseminate scientific knowledge

Why do we publish the way we publish?

What kind of publications serve our needs?

Access

Beyond the PDF

Access to what?

Scratchpad, EOL page, Wikipage, species page

Treatment

Treatments come with a lot of overhead

Genus Diagnosis Notes Biology Distribution Key to sp. Species descriptions The structure of a systematics publication Species treatments Title Author Abstract Introduction Taxon descriptions Suppl. Materials Acknowledgments References Species 1 Species 2 Species 3 Species 4 Species .. Species n Nomenclature Diagnosis Distribution Material Examined Comments Description Graphic art Species 1

Treatments come with a lot of overhead Treatments are highly structured

Genus Diagnosis Notes Biology Distribution Key to sp. Species descriptions The structure of a systematics publication Species treatments Title Author Abstract Introduction Taxon descriptions Suppl. Materials Acknowledgments References Species 1 Species 2 Species 3 Species 4 Species .. Species n Nomenclature Diagnosis Distribution Material Examined Comments Description Graphic art Species 1

Treatments come with a lot of overhead Treatments are highly structured Content ist defined

Treatments come with a lot of overhead Treatments are highly structured Content ist defined XML can define it

This can also be applied to entire sections of text, such as the descriptions of a species and its parts. <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>

Treatments come with a lot of overhead treatments are highly structured Content ist defined XML defines them The question is, how to get them

Mark-up of legacy publications

$$$$$$$$$$$$$$$$$

Prospective semantic mark-up and linking to external sources is the future

Treatment repository + external resources

BHL-Modern

The future is writable.

Happy Birthday! January 15, 2001

What is a scientific publication? Wikipedia entry as a publication?

Quality control

What is a scientific publication? Centrifugal versus centripetal forces or are we attractive enough?

Continuity

$$$$$$$

http://plazi.org Thank you very much! Donat Agosti [email_address]

Setting the Scene for ViBRANT – Strategy, Philosophy and Communication

by vbrant on Jan 24, 2011

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