D3.3.2 - Report on progress during the coordination process of partners and non consortium partners

The report has been submitted on April 30, 2014, and is also available here.

About

One of the pro-iBiosphere Deliverables is D3.3.2, a report on progress during the coordination process of partners and non consortium partners (due by April 2014).

A workshop was held in February 2014 (MS12) to discuss and coordinate with partners and non consortium partners the implications of D3.3.1. The aim of the workshop was to build consensus on the recommendations and next steps for the semantic enrichment and integration of legacy biodiversity literature. The deliverable will summarize the outcomes of the workshop and build on D3.3.1 to generate a workplan and roadmap for the semantic integration of biodiversity literature.

Notes

See also the notes for D3.3.1.

GDocs from the workshop

• notes
• questionnaire
  • responses

Additional references

See also https://en.wikipedia.org/wiki/User:Daniel_Mietchen/Semantic_integration_of_the_biodiversity_literature .

• GDoc sketch
• Knowledge Extraction and Semantic Annotation of Text from the Encyclopedia of Life
• D4.2
• Brian L. Pytlik Zillig, « Logging the Abbot: Reflection-Oriented XSLT Programming for Corpora Conversion and Verification », Journal of the Text Encoding Initiative [Online], Issue 4 | March 2013, Online since 27 February 2013, connection on 04 February 2014. URL : http://jtei.revues.org/722 ; DOI : 10.4000/jtei.722
• Biodiversity Data Integration Interest Group
• Automated Annotation of Scientific Documents: Increasing Access to Biological Knowledge
  • With section on future developments
• Twitch Crowdsourcing
• Marakeby H, Badr E, Torkey H, Song Y, Leman S, et al. (2014) A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature. PLoS ONE 9(2): e89142. doi:10.1371/journal.pone.0089142
• Transcribe Bentham
• Label transcriptions
  • Many label texts transcribed in papers like this one
• NHM outlook
• Target 19 of the Aichi targets

  "By 2020, knowledge, the science base and technologies relating to biodiversity, its values, functioning, status and trends, and the consequences of its loss, are improved, widely shared and transferred, and applied. "

• Purposeful gaming at BHL
• More on discovery mechanisms at BHL platform
• Denny Vrandečić, Markus Krötzsch. Wikidata: A Free Collaborative Knowledge Base. In Communications of the ACM (to appear). ACM 2014.
• LINKED GEO DATA
• Biological Collections Ontology
• markup at EOL
• Open Tree of Life
• hypothes.is
  • once more
• Annotopia
• Visualizing text
• PeerLibrary
• Optical Society of America have converted all of their backfiles (i.e. back until 1918) into JATS, cf. JATS-Con talk
• JATS-like tagging suite for books: BITS - cf. JATS-Con talk
• MathML

  MathWebSearch

  MathOverflow

• "Markup systems and the future of scholarly text processing” from 1987
• Semantic integration in Geosciences
• Dealing with markup semantics
• "as scientific ontologies are integrated into the publishing workflow"
• 2003 book: Intelligent Search on XML Data
• PMC-Europe
• MPDL
• TEI

  https://www.ncbi.nlm.nih.gov/books/NBK47113/

• Tim Berners-Lee, James Hendler and Ora Lassila, "The Semantic Web", Scientific American, May 2001, p. 29-37.
• Competency Questions for RDF Treatments
• Biomedical ontologies
  • http://www.jbiomedsem.com/content/5/1/15/abstract
• Semantic technologies in healthcare and life sciences
  • http://www.jbiomedsem.com/series/SWAT4L2013
• The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
  • http://www.jbiomedsem.com/content/4/1/6
• BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
  • http://www.jbiomedsem.com/content/5/1/5
• Biomedical Semantics: the Hub for Biomedical Research 2.0
  • http://www.jbiomedsem.com/content/1/1/1
• OBO Foundry
  • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814061/