Minutes. Date: Location: UCSD BRF2 5A03. Attendees Present

Transcription

1 Executive Committee Meeting Location: UCSD BRF2 5A03 Date: Start time: 10:00 am PDT End time: 11:30 am PDT Meeting Objective Attendees Present Minute Taker Executive Committee Meeting UCSD: Lucila Ohno-Machado, Claudio Farcus, Jeff Grethe, Elizabeth Bell, Stephanie Hagstrom UTHealth: Anupama Gururaj Michigan: George Alter Oxford: Susanna Sansone Diana Guijarro, Elizabeth Bell Agenda Item #1 Items Minutes All- Hands Meeting Sept 11 th Sheraton Downtown Denver Agenda Shown is the agenda that Ron made some edits on and asked us if the edits he and other NIH members made were acceptable We combined some core dev and demonstrations in the longer session in the morning and have the collaboration with longer session in the afternoon instead of being in separate category also have a new discussion for the deliverables for year 3. Does anyone have an input? Lucila: not sure if we can issue the agenda like that before having consulted BD2K if they can be there. Elizabeth sent s to Pepei but no respond back We were all cc ed on Ron comments We can try but it seems odd that this discussion will come and then we will discuss our deliverables and the people need to come back at 4pm again- doesn t make sense Recommend to switch the order to put our deliverables first and then collaborations at the end Can have a close session as well from 8-9am, since most of the people are coming the day before- and maybe we can discuss the deliverables at that time. At that point we will have information of the supplements and approvals Anyone have some conflict with the timing for the agenda? Since there is no conflict we will keep 9-6pm o Update on NLP Challenge Draft of the timeline of the NLP challenge Anu sent out in google doc

2 Do people have any changes they suggest? Only George and Susanna has made changes Please look at it and send your feedback Prety soon we need to start setting up the website- have the dataset ready for distribution and will be done with the benchmark next week and the queries all set up and ready to go. We are set in terms of running the challenge- wanted to have an input from the EC Lucila will look at the google doc today Anu: Where do we want to send this out to? Lucila: BD2K has a weekly announcement, to the NLP mailing list (Hua belongs to a couple of those) and Lucila can try one more venue. o Revised paper Lucila forwarded the comments she received to the EC. Lucila will keep us posted if she gets any reviews- will probably need another revision Received a comment back from one of the editors saying we should focus the paper on the datamed and not the data discovery in general- suggested some removals- forwarded the comments to everyone- still time to change, it is just a submission In order to make it a joint author submission that would acknowledge the people- if we created a joint authorship named biocaddie team would have to submit everyone in that list, get their approval and include them in the biocaddie authorship. There are pros and cons- need some suggestions The list that we have in the end- the only thing is that she didn t replicate names if one member is in another WG too. If everyone could please look at it and see if she missed somebody We have time to decide if we should do a set there would be logistics involved; in trying to contact everyone and see if they want to be acknowledged or not. Had to remove some stuff- maybe can use in another more informal paper Need to think of the specialized paper- the ones that are more detailed. What does everyone think of that?- it s not on the white paper o Pilot projects Got an update from Dr. Gouripeddi about their pilot project- said they are now completed except for the literature write up, will let us know when they are being submitted and accepted Dr. Mungall pilot is still on track to be completed by October Agenda Item #2: Core Dev Updates Reconciliation of indices with WG3 metadata mode v2 o Had a call on Thursday with Philippe and Alejandra to discuss some of the

3 last points o Decided to start generating some review documents using the full pipelinewhich means the metadata reconciliation with all the enhancement modules we have been working on. o Will be sending out the review docs to Philippe and Alejandra by tomorrowwill be a final review check- by that point we can have V2 of the whole indexing pipeline complete, tested and reconcile with DATS and can start pumping the new and old data sets. Data Set Ingestion o Remapping of previously ingested repositories to DATS 2.0 o Documentation of ingestion pipeline o Lucila: we haven t yet made a process that makes the different groups that are working independent. Suggests that Hyeon-eui, Jeff and Anu to meet and divide the work so we can ingest more datasets we are currently doing. Would like between now and all-hands if we can show this is the current state. CEDAR o Working with Cedar template for biocaddie dataset- have a call with CEDAR today o Will review that on the call today with other questions one of the questions is how do we want to get into the form online for metadata to be filled out by users for datasets UI Development o Still working on improving on the response time o Technical meeting on Tuesday gave them some feedbacks on the visualization- will try to finalize the visualization that we would like to incorporate into the UI side o Also looking into using Linkout to drive more traffic to DataMed - also being discussed in the CDT meeting today is: o Claudiu has re-routed datamed.biocaddie.org to datamed.org - so have no more traffic on the datamed.biocaddie.org o The google analytics tells us that we still have a fair amount of traffic not only in the US, but also in Europe and Asia- which is good 2016 biocaddie DataSet Retrieval Challenge o would like to get feedback about the NLP challenge on the google doc Ontology web services o The terminology server has been integrated at the UI side Benchmark dataset generation/ System Evaluation: 23 repositories frozen for use o Will be done with the annotation next week- will be ready to evaluate for the current elastic search as well as for provided to the challenge Usability & Testing Had some feedback from WG9- have modified the questioner that we plan to send out as part of phase I Working next is on generating a draft of the summative testing that

4 is going to be done- that is actually Phase III of user testing Meeting with WG 11 o To generate SOP for repository submission form Pilot project integration o Have started with the pilot project integration o Last week we had a presentation by Gouqian; scheduled a presentation by Ram at the end of September o If the Berkley group gets done by October- the next step is to have presentation to discuss how to integrate the pilot projects and their results into the prototype Issues o Updated number for the issues on the prototype that we reported o Haven t closed any usability issues since we are still discussion- will be worked on o Had limited response with reference to v.1 in terms of issues Agenda Item #3 Working Group Updates WG2: One aspect of the identifier s work was to be able to notate the repositories that served cross list contents- that s part of the full pipeline now Data Citation Implementation Pilot Working on the identifiers landing page and data citation piece of that- that document is being prepared right now with the final recommendation for that group. WG3: There are a few things that need to be finalized for the DATS v2.1 but almost there Will finalize it by this week. Will have it with the changes by next week so Jeff and Hua team can start working on. Also agreed to hold on with the release of full v2.1- because Alejandra would then have to work on shchema.org annotation and that will take an extra week. But will do the release before the All-Hands meeting in September WG4-8: Completed WG9: Had first meeting (July 22) where talked about the CDT user testing planbased on the feedback obtained plan to modify the survey that we are planned to send out as part of Phase I of user testing Working on summative testing which will be Phase III user testing need a script and modulator for that which they are working on right now; will be discussed on the 2 nd meeting Working on Scheduling the 2 nd meeting as well

5 WG11: Had a call with all the teams except with Oxford group to talk about how to manage the contacts with the repository who wanted to be included There is a document on the google drive with more details Came up with that when anyone hears from a repository, they will ask the repository to fill out the repository submission form that is on DataMed, the UT has already modified the form. with additional fields to get more background The form automatically creates an issue in GitHub that we can follow, once that is created then Sanda will make sure that it goes forward, will send an acknowledgment to the person that filled it out, assigned someone to respond to the repository and begin an evaluation process based on the criteria that came from WG 6- so the EC can assign a priority We are asking that everyone put all the information about these contacts into GitHub so can keep track on what s going on, Sanda on a weekly bases will make sure that none of them are stalled or have gotten lost. George met with Sanda and Jared: Came up with a simple version for the evaluation form; Sanda will make some examples so we can get some experience with them- and she will be contacting people. There are currently 5 repository contacts in GitHub- Jeff claimed 1 Sanda will write to all the groups and ask people to claim the ones that they have been working on so they can assign themselves as responders- so every contact has someone assigned to it. WG12: According to our white paper, WG 12 should start next month Need to keep in mind that this is coming up, figure out who will be leading it and the goals and deliverables Is anyone has any ideas/questions let Elizabeth know. Action Items Task Due Date Person Responsible Send feedback about challenge to Anu Soon All Check list of acknowledgements in biocaddie paper to make sure everyone is included tell Lucila if not Dataset ingestion people to work on aligning to work on datasets in parallel Let Sanda know if you are claiming a repository contact in Github questions or comments about starting up WG12 to Elizabeth Next Meeting: 10:00 am 11:30 am PDT on August 30, 2016 ASAP Soon Soon By end of Month All Hyeonui, Anu/Hua, Jeff All