20090921 art databanken agosti final
DESCRIPTION
Lecture presented at the ArtDataBanken meeting in Stockholm on September 21, 2009TRANSCRIPT
Literature and XML:or How to Have More Time to
Think
Donat AgostiPlazi
ArtDataBanken Stockholm, Sept 21, 2009
Who is this?What do I know about her?
Where does she live?
Who are you?What do you do?
Where are you from?
The answers are inseveral hundred million pages of printed
species descriptions in our libraries, including the descriptions redescriptions of
an estimated 1.8M species, and an estimated 50K new
(re-)descriptions annually.
Taxonomists at work ……
T. E. Lawrence: Seven Pillars of Wisdom – a triumph. 1st published for general circulation, 1935: p. 535
The traditional flux of information …
…a more or less closed, intransient system
What has this to do with XML,semantic, enhanced documents?
Access
Scanning
Pdf-conversion
(WWW)
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).
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...
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)
Can taxonomic work be copyrighted?
Copyright legislation is national but is based on the Berne Convention for the Protection of Literary and Artistic Works which defines a minimal standard. This international copyright standard does not require the recognition of treatments, the building stones of taxonomic publications, as works.
“work” does not mean “text”, does not mean “data”, does not mean “information”. A “work” is something more. That kind of something more has many different definitions in the various legislations, but it is always there: It may be called originality, individuality, creation, personal expression, creative shaping or anyhow else, but it is a condition for qualifying a product as a work: “Work” is an intellectual product that is in a certain sense particular, individual, original, new. (Egloff: EDIT IPR and Copyright, 2008)
Taxonomic treatments are highly structured and homogenous, part of a global >100 million page corpus growing at a rate of ca 20,000 new species descriptions per year, not counting 5 times more redescriptions. Its structure is tightly controlled by a peer review process enforcing standards, a domain specific vocabulary, not written as poem or in flowery language but scientific jargon.
Treatments do not qualify as work.
The publications including the treatments might.(Egloff: EDIT IPR and Copyright, 2008)
It is about digesting millions of pages:
>>100 M pages taxonomic literature
25M scientific publications / year25K journals
>1K with taxonomic descriptions
20K descriptions of new species / year
Is this is the access we need?!
No, we need open access to content, not the PDF per se.
It is about machines(not we) doing a great deal of the
work for us, extracting data, formulating hypothesis, ....
It is about data and information in context
„Nothing makes sense in biology except in the light of treatments“.
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:
27,266 papers
4,563 papers41,985 papers
10,365 papers
128,437 papers
“protein-protein interaction networks” John Wilbanks, Neurocommons
Relational to Ontological Mapping
Drug
Neuron
PathologicalAgent
Receptor
Channel
inhibitsinhibits
Agent
NeuronalProperty
PathologicalChange
involvesinvolves inhibits
Compartment
has
is_located_in
is_located_in
slide courtesy of kei chung, yale
It will open up scientific literature for data mining
“protein-protein interaction networks” John Wilbanks, Neurocommons
TREATMENT Cremastogaster mimosae Likely Diagnostically Related to: Cremastogaster tricolor Likely Diagnostically Related to: Cremastogaster tricolor Likely Diagnostically Related to: Cremastogaster amabilis Likely Diagnostically Related to: Cremastogaster tricolor Likely Diagnostically Related to: Cremastogaster amabilis Associated with: Acacia sienocarpa Living in: Mombasa Lviing in: Tanga
It is more: it is about access to the original or
source data
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.
Semantic, enhanced treatments do the job ...
... and XML is one way to go.
XML
XML stands for EXtensible Markup Language
XML is a markup language much like HTML
XML was designed to carry data, not to display data
XML tags are not predefined. You must define your own tags
(schema)
XML is designed to be self-descriptive
XML is a W3C Recommendation
XML
Being open and non-proprietary XML is an optimal archival
format for the treatment/publication
Being a stable and rich data format, XML can be repurposed for
a variety of purposes
XML
XML application design is an art in itself .... and thus can not be
explained in 15 minutes
Plenty of resources to dive into XML on Web, eg
http://www.w3schools.com/, etc.
This means to develop a schema that models the logic content (e.g TaxonX), insert those tags that define what a word means, so a computer can understand as well. To assure, that everybody talks about the same species, the name can be linked to a reference name server
Azteca instabilisTaxonx-schema
Would then read like External schema
<tax:name><tax:xmldata> Normalization of data <dc:Genus>Azteca</dc:Genus> <dc:Species>instabilis</dc:Species> </tax:xmldata>
Azteca instabilis </tax:name>
This can also be applied to entire sections of text, such as the treatment 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>
global unique identifiers (e.g. LSID) link up data
LSID for scientific publicationsLSID for treatmentsLSID for names (Zoobank/ HNS..)LSID for specimensLSID for DNA sequences / characters (ontologies)LSID for repositoriesGPS fixes for locations
Azteca instabilis
Would then read like
<tax:name><tax:xid source=“LSID" identifier=“urn:lsid:biosci.ohio-state.edu.osuc_concetps:13452"/> Link to external database <tax:xmldata> Normalization of data <dc:Genus>Azteca</dc:Genus> <dc:Species>instabilis</dc:Species> </tax:xmldata>
Azteca instabilis </tax:name>
We need XML-schemas, tools to convert and expose
semantically enhanced documents.
Plazi workflow: overviewPlazi deliverables
TaxonX XML schema
GoldenGate
Dspace application
Exist application
SRS
Exchange protocols (SPM, TAPIR, REST)
- 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
Plazi workflow: content
11,000 descriptions online500 publications4,500 publications
Handle, SPM and Tapir servicesFeeds into HNS and Zoobank (soon)Is harvested by GBIF, EOLSupport from GBIF, EOL, US-NSF, DFG
Does the retro mark-up process scale up to the millions of pages needed to be processed?
Only partially: Mark up takes about 5min/page: For 100 M pages = 700 man years (but it is only a first tool...)
Does the mark-up process scale up to the millions of page needed to be processed?
Only partially: Mark up takes about 5min/page: For 100 M pages = 700 man years (but it is only a first tool...); wizards can reduce the time by several factors
But: How much does it cost to digitize specimens, and what is its quality?
The cost of converting legacy publications can be avoided by
producing marked-up publications up-front
NLM/TaxonX schema allows publishers to maintain richly encoded articles whose data can be distributed and presented in multiple formats for a
variety of uses.
NLM/Taxonx XML Document
NLM/Taxonx XML Document
NLM/Taxonx XML Document
HTML
NLM/Taxonx XML Document
HTML
SPM /RDF
SPM /RDF
SPM /RDF
NLM/Taxonx XML Document
HTML
SPM /RDF
Database
HTML /Species Page
HTML
SPM /RDF
SPM /RDF
HTML /Species Page
HTML /Species PageEg. EOL, scrathpads
NLM/Taxonx XML Document
HTML
SPM /RDF
Database
HTML /Species Page
LSID resolver
HTML
SPM /RDF
SPM /RDF
HTML /Species Page
HTML /Species PageEg. EOL, scrathpads
NLM/Taxonx XML Document
HTML
SPM /RDF
Database
HTML /Species Page
Dataminig, ...
LSID resolver
HTML
SPM /RDF
SPM /RDF
HTML /Species Page
HTML /Species PageEg. EOL, scrathpads
Semi-automatically generated semantic, enhanced
e-publications are the only way to describe the missing 10 M species, and
to deal with an increasing flood of data.
ms submission(„Taxon-x-version“)
new ms alertPosting for review
Edited ms
Revised msPublication: pdf
Publication: hard copy
Publication database(„taxon-x-version“)
ontology
bibliography
analysis & ms preparation
ZooBank / NS
Character DB
Specimen DB
Description DB
Distribution DB
Char. Matrix DB
Phyl. Tree DB
Char-state Im.
Specimen Im.
Habitat Image
Leg. Publicat.
Tax
on D
B
New Data
feedback
Accepted ms
New taxon alert
The future of publications: The publication semiautomaticall generated
Word MS
DB
Input forms
export
export
convert NLM taxpubIndesign
NLM taxpub
author
author
author
publisher
publisher
publisher
Journal authoring and production workflow
Ctd.
NLM/Taxonx XML Document
HTML
SPM /RDF
Database
HTML /Species Page
Dataminig, ...
LSID resolver
HTML
SPM /RDF
SPM /RDF
HTML /Species Page
HTML /Species PageEg. EOL, scrathpads
Ctd.
Word MS
DB
Input forms
export
export
convert NLM taxpubIndesign
NLM taxpub
author
author
author
publisher
publisher
publisher
Journal authoring and production workflow:
What do we miss?
available
prototypes
to be developed
Where do we stand?
2008LSIDs, external links
Where do we stand?
2008LSIDs, external links, XML
Where do we stand?
2008
Where do we stand?
2009
LSIDs, external links, external data via doi, export services
Where do we stand?
2009LSIDs, external links
Recommendations:
Individual levelAssure that all you do is open access• Understand copyright – be not afraid of copyright• Self archive (the Green Road)• Create content for the Web
Self archive (the Green Road): UNIZ as one of the global leaders in self archiving
Recommendations:
Individual levelAssure that all you do is open access• Understand copyright – be not afraid of copyright• Self archive (the Green Road)• Don‘t sign any contracts giving away rights• Talk to your scientific societies and museum to adopt a policy to
at least allow self archiving• Demonstrate the power of access through inovative research
projects and data: Research will be the only motivation to change law and build up infrastructure
OECD Declaration for Access to Research Data from Public Funding
(Spring 2007)
How to implement this?
Recommendations:
• Assure that all you do is open access• Understand, adopt and propagate an adequate copyright policy• Talk to your scientific societies and museum to adopt a policy to
at least allow self archiving• Talk to your publishers to move into XML publishing• Support the emergence of standards and transfer protocols
Recommendations: (ctd.)• Science policy has to change to build and maintain the
necessary cyberinfrastructure, similarly to the building of libraries
• Prospective publications must be structured to allow machines to read and understand them.
• Copyright must be adjusted to accomodate ingenious and best useage of our shared knowledge, such as using Creative Commons licencies or applying the principles of the Conservation Commons.
• Sharing data has to become standard practice between scientists
Recommendations: (ctd.)• Science policy has to change to build and maintain the
necessary cyberinfrastructure, similarly to the building of libraries
• Prospective publications must be structured to allow machines to read and understand them.
• Copyright must be adjusted to accomodate ingenious and best useage of our shared knowledge, such as using Creative Commons licencies or applying the principles of the Conservation Commons.
• Sharing data has to become standard practice between scientists
antbase.org: Freier Zugang als Grundlage…
