Call for Proposals

BLAH3 is organized as an open forum for collaborative development of software, data sets, specifications, and so on, for linked biomedical annotations to literature. However, the first-day symposium is planned to be a venue for exchanging ideas and visions for the hackathon and the future of the community. For the program of the symposium, and for collaboration during hackathon, we solicit proposals for contribution.

  • Submission due: 18th November, 2016
  • Notification : 30th November, 2016

The submissions will be reviewed to determine their suitability for BLAH, and selected proposals will be presented for the first day symposium. We expect successful proposals to find interested participants who will collaborate on them during the hackathon. The authors of selected proposals also may apply for travel supports.

The types of contributions may include, but not be limited to

  • Annotation data sets
  • Tools for annotations
  • Applications of linked annotations
  • Userbility tests
  • User interface issues
  • Reproducibility issues

Annotation data sets

For annotation data sets, we particularly focus on annotations to 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). 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 (Creative Commons preferred)
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.

Expected types of annotations to be submitted may include, but not be limited to:
  • Manual or automatic annotations
  • Semantic or syntactic annotations
  • Biological or clinical annotations

Tools for literature annotation

We also solicit tools and systems for production of literature annotation which will wiilingly be publicly available. Prospective tools will be supported to be made inter-operable with other tools (mainly through REST API and JSON).

As an example, a way of linking an automatic annotation tool from PubAnnotation is described in this document.
Also, a way of making an annotation editor compatible with PubAnnotation is described in this document.

Expected type of contribution will include, but not limited to:
  • visualization (e.g., TextAE)
  • automatic annotation (e.g., TagTog)
  • format conversion (e.g., simple_bioc)
  • evaluation
  • 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 to the public,
    • open-source software is desired.
  • provide RESTful APIs for programmable access, and
  • provide comprehensive online documentation.
Alternatively, and more ideally, a homepage may be prepared with descriptions of all the above aspects. In that case, simply the URL of the homepage can be submitted.

Applications of linked literature annotation

To promote next generation text mining research based on the linked literature annotation resources, we also call for position papers to present innovative ideas 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 of 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.

It is expected that successful proposals shall present
  • novelty
  • feasibility
  • proof-of-concept examples
  • data sets to be used (if 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).