...
October 2018
Present: Vincent, Dave, Anna, Terry, Boris, Andrew, Yves, Friedrich, Richard.
Summary: summarised in Biologics DB Collaboration landing page
...
December 2018
Present: Dave, Terry, Boris, Yves, Richard.
Summary:
Data and availability:
...
ACTION: all to share feedback on AbVance II proposal with Richard by email (https://pistoiaalliance.atlassian.net/wiki/download/attachments/92307462/AbVance%20II%20partner%20proposal%20October%202018%20FINAL.pdf?version=1&modificationDate=1541770378626&cacheVersion=1&api=v2)
...
February 2019
Present: Vincent, Terry, Boris, Andrew, Yves, Friedrich, Richard.
Summary:
Options for an open access "biotherapeutics ChEMBL" resource - Andrew and Friedrich:
...
April 2019
Present: Dave, Boris, Andrew, Yves, Richard.
Summary:
...
June 2019
Present: Dave, Boris, Andrew, Yves, Richard.
Summary:
Update on search term capabilities
>Dave has shared additional publications with high quality PK (likely Tier 1) and a starting set of search terms (need to be added to the wiki space)
>Andrew and Anna are planning data extraction from papers based on the above but this has to be manageable and needs to be resourced by existing funds. In this context some Q's still need to be addressed:
- What is the feasibility of extracting this kind of data vs SM data?
- Will ChEMBL data model match onto this kind of data?
- Looking ahead: what is the broader scope (see below)? does more automated identification of literature fit into the workflows which have been already developed for ChEMBL? and what funding model will support this?
>We need a consensus on what is a meaningful, manageable and affordable pilot study but for this to be useful to as many people as possible, without sacrificing quality and relevance, there should be 2 components: PK data described above and more biophysical data as described in the Jain paper. These should be included in the list on the wiki.
>A first pass pilot study (PoC) needs to successfully identify relevant data based on search terms and will not necessarily give insight info confounding factors, issues etc. which would help the users/searchers of the information.
...
ACTION - Dave and Boris to upload a couple of further papers which have been identified.
ACTION - Dave to upload proposed 'search terms'.
ACTION - Friedrich to update sources of Biophysical data to cross-reference
ACTION - Andrew to let us know when it would be feasible to have resource to establish a working prototype (PoC) and hence inform the timelines for running the workshop
Update on search term capabilities
>Dave has shared additional publications with high quality PK (likely Tier 1) and a starting set of search terms (need to be added to the wiki space)
>Andrew and Anna are planning data extraction from papers based on the above but this has to be manageable and needs to be resourced by existing funds. In this context some Q's still need to be addressed:
- What is the feasibility of extracting this kind of data vs SM data?
- Will ChEMBL data model match onto this kind of data?
- Looking ahead: what is the broader scope (see below)? does more automated identification of literature fit into the workflows which have been already developed for ChEMBL? and what funding model will support this?
>We need a consensus on what is a meaningful, manageable and affordable pilot study but for this to be useful to as many people as possible, without sacrificing quality and relevance, there should be 2 components: PK data described above and more biophysical data as described in the Jain paper. These should be included in the list on the wiki.
>A first pass pilot study (PoC) needs to successfully identify relevant data based on search terms and will not necessarily give insight info confounding factors, issues etc. which would help the users/searchers of the information.
>Way forward proposal from Boris (see slides below)
...
- Our application would fall under the category of domain-specific software for analyzing, visualizing, and otherwise working with the specific data types that arise in biomedical science (e.g., genomic sequences, microscopy images, molecular structures).
- We would likely aim for the 1 February 2020 deadline
- Funds ($50-250k) are for 1 year and cover a range of uses including salaries, workshops, operational needs, etc.
ACTION - Dave and Boris to upload a couple of further papers which have been identified. Dave - upload proposed 'search terms'.
ACTION - Friedrich to update sources of Biophysical data to cross-reference
...
- We would likely aim for the 1 February 2020 deadline
- Funds ($50-250k) are for 1 year and cover a range of uses including salaries, workshops, operational needs, etc.