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:
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 contribution 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 output 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 (to the Covid-19-related literature)
Integration of annotation tools
provision of terminology resources
exploration of use cases of the collection of Covid-19 annotation datasets
implementation of resources for scalability, sustainability, or FAIRness of annotation data or tools
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.
Registration of participation
Registered participants will be included in the mailing list of BLAH7, to which important messages for participation will be posted, they also will be invited to the slack workspace of blah7.
Please carefully keep the confirmation mail which you shall received soon after the completion of your registration, as the mail includes a link for edition of your registration.
Registration of projects
If you want to register a project for hackathon, (1) please create a home page of the project (e.g., using a GitHub repository), and (2) indicate the URL of the project homepage during your registration of participation. If you are not yet ready with your project homepage, or you are not sure if you will register a project, you can still make your registration of participation without project registration. Later, when you are ready, you can make your project registration (by editing your registration of participation with your project information). To do so, you have to carefully keep the confirmation mail of registration, which contains a link to edit the registration. A project homepage is supposed to be used to introduce other participants to the project, to facilitate communication among collaborators, and to wrap-up intermediate and final results. All the registered projects will become visible to the registered participants, so that participants can find their interested projects.
After the hackathon, a journal special issue (see below) will be organized to publish outputs of BLAH7. For your reference, the special issues of previous BLAH events can be found below:
How will the (online) hackathon work
The organizing committee will organize three plenary (online ) meetings for (1) project presentations, (2) Intermediate updates, and (3) final wrap-ups. Considering that they will be held as online meetings and the diverse time zones, we would like to minimize the length of the meetings, and they will be held as follows.
Project presentation meeting (18th)
The projects that are registered by Dec. 4th will become candidates for the plenary project presentation meeting. The PC will review the project homepages and deliver comments by Dec. 25th. Inclusion of the projects in the project presentation meeting will be confirmed by Dec. 29. For every project to be presented in the project presentation meeting , an introductory video clip should be registered by Jan. 8. The video clip should include a full presentation of the project so that other participants can understand the project and can send questions, comments, or proposal of collaboration. Each presentation (~10 minutes) in the plenary meeting should consist of a short introduction, answers to the questions and comments, and prospective collaborations during the hackathon.
Intermediate update meeting (20th)
Progress report and change (drop, merge, creation) of projects will be shared among the participants.
Final wrap-up meeting (22nd)