[BLAH] Calls, the 7th Biomedical Linked Annotation Hackathon (BLAH7)

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TAKATSUKI Terue

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Oct 28, 2020, 9:13:12 PM10/28/20
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Dear all,

The 7th Biomedical Linked Annotation Hackathon (BLAH7)

- When: 18 - 22 January, 2021
- Home: https://blah7.linkedannotation.org
- To be held as an online event

BLAH (Biomedical Linked Annotation Hackathon) is a series of hackathon
events which is annually organized to promote an open collaboration
for making a breakthrough in sharing and linking resources for
biomedical literature annotation and mining, and thus for improving
interoperability among those resources. Here, interested resources
include corpora, annotation datasets, databases, software tools, web
services, terminologies, ontologies, graphics, movies, and so on. We
hope they are all to be linked to each other in an interoperable way,
which we believe will substantially improve the productivity and
impact of the community.

BLAH7 (the 7th BLAH) is organized with a special theme "Covid-19",
with a goal to find an answer to the question

“How far natural language processing (NLP) technology can help
fight Covid-19, if forces are joined?”

Due to the current pandemic situation, BLAH7 is organized as an
online event. As an online hackathon event, to make the efforts more
focused, and to widen the chance of participation, at the same time,
we are going to get focused on LitCovid, a collection of
Covid-19-relevant documents, which is compiled and released by NCBI,
and to prepare annotations for fundamental biomedical entities, based
on at least three automatic annotation resources, PubTator (NCBI),
OGER (IDSIA), and PubDictionaries (DBCLS) (suggestion with other
resources is welcome). Beginning with the already richly annotated
literature collection, through BLAH7, we would like to see what kind
of additions will make what kind of contributions. Note that as
annotations for fundamental biomedical entities will be given,
additional contributions do not need to necessarily address
biomedical aspects. For example, annotations for following aspects
are not specific to biomedical aspects, they shall be highly useful,
if they can be added:

- quantifications
- qualifications
- timings
- speculations, and negations
- ...

Of course, annotations for other biomedical aspects are welcome, e.g.

- other types of entities
- relations between or events on biomedical entities

We also would like to explore how such integrated various annotation
resources can be used to help fight Covid-19. Note that as a
hackathon event, we are more interested in synergic contributions,
rather than contributions by individual resources. For effectiveness of
the collaboration, we are also interested in investigating the
following three sub-themes:

- Scalability: as the scale of relevant literature is millions,
annotation resources should be capable of handling that scale to make
a practically meaningful contribution.

- Sustainability: as Covid-19-related literature is rapidly
increasing, we need a sustainable framework to maintain annotation
up-to-date

- FAIRness: as one of the outputs of BLAH7, we are aiming at
producing a collection of annotation resources. To improve the
usability of the resources, we are interested in improving the
FAIRness of them. (See the FAIR data principles:
https://www.force11.org/group/fairgroup/fairprinciples)

# Call for hackathon projects and participation

We invite participation of researchers or practitioners who are
interested in contributing with their literature annotation resources,
or expertise. For the hackathon, there will be participants who will
initiate projects, and those who will join projects initiated by
someone else, which are all welcome, as a hackathon is all about
facilitation of collaboration. We invite projects which can be
accomplished during the hackathon. The type of contribution may
include, but not restricted to

- Integration of annotation data
- Integration of annotation tools
- Development of terminology resources
- Exploration of use cases of the Covid-19 annotation collection
- Development of resources for scalability, sustainability, or
FAIRness of annotation data
- ...

While we are not going to restrict the type of contribution strictly,
in case you are not sure whether your contribution will be relevant to
Covid-19, you are encouraged to think about if there is at least an
indirect potential connection between your resources and helping fight
Covid-19.

# Important Dates

- Registration of projects due: 4th (Friday) December, 2020
- Registration of participation: 8th (Monday) January, 2021

# Program Committee

- Jin-Dong Kim, DBCLS
- Kevin Bretonnel Cohen, Univ. Colorado
- Zhiyong Lu, NCBI
- Fabio Rinaldi, IDSIA


Kind regards,
Terue Takatsuki on behalf of the BLAH 7th organizers
Database Center for Life Science, Japan
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