Call for contributions

Call for text annotations

We solicit text annotations of PubMed or PubMed Central (PMC open access subset) articles (e.g. the NCBI disease corpus which contains disease annotations of 793 articles). Submitted literature annotations (a.k.a. corpora) will be linked with each other, and made freely available for public use (examples of linked annotations can be found at the PubAnnotation homepage). Also, all the annotations will be indexed using semantic web technology and will become searchable and accessible through SPARQL and REST API. Being linked with others, any annotation data set will find a significantly improved value of its own (like any document linked with others in WWW). The contributors will retain the full credit and right to their data sets. Any usage of the data sets will be asked to make proper citations.

Prospective contributors are asked to submit a description of the data sets (1-2 pages) which should include:

  • name of the text annotation data

  • the name and e-mail address of the contact person(s)

  • how the base texts are collected

  • how the annotations are developed, e.g., manually or automatically

  • a small piece of example and a detailed description of it

  • reference to relevant publications or web pages if any

  • license policy (in terms of creative commons, hopefully)

Alternatively, and more ideally, a homepage may be prepared with descriptions of all the above aspects. In the case, simply the URL of the homepage can be submitted.

The submissions will be reviewed to determine their suitability for BLAH. Successful contributors will be asked to schedule a couple of days in January or February of 2015 to collaborate with the organizers to have their annotations submitted, and linked, before the BLAH hackathon.

Contributed text annotations will be listed on the hackathon homepage and in the joint paper. Contributors will be invited to attend the BLAH hackathon/symposium, to discuss and hack for further integration, publication, and application of the linked resources.

Expected types of annotations to be submitted may include, but are not limited to:

  • Manual or automatic annotations

  • Semantic or syntactic annotations

  • Biological or clinical annotations

Call for position papers (extended abstracts)

In addition to collecting and linking together various annotations made to PubMed and PMC articles, promoting next generation text mining research based on the new resources will be another aspect of the event. In the regard, we call for position papers to present innovative idea of utilizing or extending the potential of the linked annotation resources.

Scope of interest may include but not be limited to:

  • applications which can be linked to biologically or medically meaningful discoveries

  • integration to existing workflows

  • tools for utilization of linked resources, e.g., analysis, visualization, conversion, mining

A submission may consist of up to 1000 words with figures and tables. A submission shall be a PDF file which includes all the figures and tables.

All submissions will be peer-reviewed by the Program Committee, and accepted ones will be published in a special issue of BMC proceedings (PubMed-indexed).

It is expected that successful proposals shall present

  • novelty

  • feasibility

  • proof-of-concept examples

  • data sets to be used (in case the data sets are developed by other groups, submitting a joint proposal is recommended)

For each accepted proposal, it is expected that at least one author shall attend the BLAH hackathon/symposium to present the work to seek potential collaboration with other meeting attendees (e.g. data providers).

Call for tools or systems

We also solicit tools and systems to be integrated in the hackathon environment before the BLAH hackathon. Prospective contributors will have to collaborate with the organizers to make their tools inter-operable with other tools (mainly through REST API and JSON). Successful contributions will be provided to the participants (and also to the public), listed in the hackathon homepage and in the joint paper. Any usage of the tools will be asked to make proper citations. The contributors will retain full credit and right over their tools and systems.

Expected type of contribution will include, but not limited to:

  • visualization

    • analysis

    • format conversion

    • mining

Prospective contributors are asked to submit a description of the tools (1-2 pages) with reference to relevant publications if any.

Successful contributions must

    • be web-based applications,

    • guarantee free access without restriction by the public,

      • open-source software is desired.

  • provide RESTful APIs for programmable access, and

  • provide online comprehensive documentation.