|
|
Line 2: |
Line 2: |
| |- | | |- |
| ! scope="row" | Session | | ! scope="row" | Session |
| | [[session::ODK]] | | | [[session::Modules and Patterns]] |
| |- | | |- |
| ! scope="row" | Duration | | ! scope="row" | Duration |
| | [[duration::1.5 hour]] | | | [[duration::1 hour]] |
| |- | | |- |
| ! scope="row" rowspan="3" | Date/Time | | ! scope="row" rowspan="3" | Date/Time |
| | [[has date::08 Feb 2023 17:00 GMT]] | | | [[has date::08 Mar 2023 17:00 GMT]] |
| |- | | |- |
| | 9:00am PST/12:00pm EST | | | 9:00am PST/12:00pm EST |
Line 15: |
Line 15: |
| |- | | |- |
| ! scope="row" | Convener | | ! scope="row" | Convener |
| | [[convener::JamesOverton|James Overton]] | | | [[convener::GaryBergCross|Gary Berg-Cross]] |
| |} | | |} |
|
| |
|
Line 22: |
Line 22: |
|
| |
|
| == Agenda == | | == Agenda == |
| * The Ontology Development Kit (ODK) | | * '''[[GaryBergCross|Gary Berg-Cross]]''' ''[https://bit.ly/3F3XKSI Why ODPs?]'' |
| * Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron
| | * '''[[CoganShimizu|Cogan Shimizu]]''' ''Modular Ontologies and Design Patterns'' |
| * [https://bit.ly/40MyKsj Slides]
| | * [https://bit.ly/3YAi6Ka Slides] |
| * [https://bit.ly/3Xo8ku6 Setting up your own repository] | |
| * [https://bit.ly/3YDzVIJ Video Recording] | |
|
| |
|
| == Conference Call Information == | | == Conference Call Information == |
| * Date: '''Wednesday, 08 Feb 2023''' | | * Date: '''Wednesday, 08 Mar 2023''' |
| * Start Time: 9:00am PST / 12:00pm EST / 6:00pm CST / 5:00pm GMT / 1700 UTC | | * Start Time: 9:00am PST / 12:00pm EST / 6:00pm CST / 5:00pm GMT / 1700 UTC |
| ** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=02&day=08&year=2023&hour=12&min=00&sec=0&p1=179 World Clock] | | ** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=03&day=08&year=2023&hour=12&min=00&sec=0&p1=179 World Clock] |
| * Expected Call Duration: 1.5 hour | | * Expected Call Duration: 1 hour |
| {{:OntologySummit2023/ConferenceCallInformation}} | | {{:OntologySummit2023/ConferenceCallInformation}} |
|
| |
|
| == Attendees == | | == Attendees == |
| * [[AleixPuig|Aleix Puig]]
| |
| * [[AlexanderDiehl|Alexander Diehl]]
| |
| * [[AlexShkotin|Alex Shkotin]]
| |
| * [[AllenBaron|Allen Baron]]
| |
| * [[AndreaWesterinen|Andrea Westerinen]]
| |
| * [[AnitaCaron|Anita Caron]]
| |
| * [[ArwaIbrahim|Arwa Ibrahim]]
| |
| * [[BartGajderowicz|Bart Gajderowicz]]
| |
| * [[BobbinTeegarden|Bobbin Teegarden]]
| |
| * [[ClaudiaSanchezBeatoJohnson|Claudia Sanchez-Beato]]
| |
| * [[CMAlvarez|C.M. Alvarez]]
| |
| * [[DamianGoutteGattat|Damian Goutte-Gattat]]
| |
| * [[FanLi|Fan Li]]
| |
| * [[GaryBergCross|Gary Berg-Cross]]
| |
| * [[JamesOverton|James Overton]]
| |
| * [[JenniferGiron|Jennifer Girón]]
| |
| * [[JieZheng|Jie Zheng]]
| |
| * [[JimBalhoff|Jim Balhoff]]
| |
| * [[JinjingGuo|Jinjing Guo]]
| |
| * [[KenBaclawski|Ken Baclawski]]
| |
| * [[MikeBennett|Mike Bennett]]
| |
| * [[NancyWiegand|Nancy Wiegand]]
| |
| * [[NicoMatentzoglu|Nico Matentzoglu]]
| |
| * [[PhilippeRoccaSerra|Philippe Rocca-Serra]]
| |
| * [[PhilipStroemert|Philip Strömert]]
| |
| * randi
| |
| * [[RaviSharma|Ravi Sharma]]
| |
| * [[RayStefancsik|Ray Stefancsik]]
| |
| * [[RobertRovetto|Robert Rovetto]]
| |
| * [[SabrinaToro|Sabrina Toro]]
| |
| * [[StefanoDeGiorgis|Stefano De Giorgis]]
| |
| * [[SydneyCohen|Sydney Cohen]]
| |
| * [[UgurBayindir|Ugur Bayindir]]
| |
|
| |
|
| == Discussion == | | == Discussion == |
| [11:56] RaviSharma: welcome everyone
| |
|
| |
| [12:07] RaviSharma: Nico, So we find common word in two or more ontologies but do not we have to also see that content meaning of blood constituents are also the same?
| |
|
| |
| [12:10] RaviSharma: Nico, we like the common infrastructure with tools that gives stability like the Operating systems did in early computing
| |
|
| |
| [12:11] James Overton: Ravi: The import system is built on identifiers (CURIEs/IRIs) not labels. So we would ask for UBERON:0000178 'blood'
| |
|
| |
| [12:17] RaviSharma: Damien, does github provide or your team has a regular compatibility check or do you execute scripts for Make to test integrability?
| |
|
| |
| [12:20] James Overton: Ravi: ODK uses GitHub Actions for continuous integration testing, which calls Make tests: https://github.com/INCATools/ontology-development-kit/tree/master/.github/workflows
| |
|
| |
| [12:27] RaviSharma: Damien - are the output files run by a user tagged so that there is versioning by users running similar commands?
| |
|
| |
| [12:28] RaviSharma: how different commands are available and is there a ? option!
| |
|
| |
| [12:30] Allen Baron: Great question and very clear explanation. Thanks Damien.
| |
|
| |
| [12:32] From Nico Matentzoglu: Damien, maybe we could run “./run.sh ls /tools/“ to get a good set of most apps, and also “./run.sh pip list” for the python stuff, and we could perhaps curate a `/tools/help` script prints these..
| |
|
| |
| [12:32] James Overton: Ravi: ODK does not tag files. We rely on git for version control, and branch-and-merge workflows, usually supported by GitHub or GitLab.
| |
|
| |
| [12:33] James Overton: Damien's answer for Ravi: The ODK paper includes a list of all the included tools, but it would be good to add a documentation page with a list of common ODK tools/commands.
| |
|
| |
| [12:35] Damien Goutte-Gattat (FlyBase): `help` would conflict with the shell builtin of the same name. But overall, yeah, some kind of inline help would be good.
| |
|
| |
| [12:44] David Osumi-Sutherland: Damien, maybe we could
| |
|
| |
|
| |
| [12:40] RaviSharma: Philip - what are the minimum metadata beside ID of ontology so the rest are taken as defaults, as many users may not have knowledge of ODKfull?
| |
|
| |
| [12:45] RaviSharma: Philip great comment about refresh version, but how do you handle compatibility between older versions of out integration namely provenance compatibility?
| |
|
| |
| [12:51] RaviSharma: For Anita or any presenters - do you have places where you store error files?
| |
|
| |
| [12:55] Sydney Cohen: is there anywhere to find a more detailed report for the violations of the SPARQL checks?
| |
|
| |
| [12:55] Sydney Cohen: would that go into the reports folder?
| |
|
| |
| [12:56] James Overton: The built-in ROBOT report commands each have a page with "problem-solution" documentation: http://robot.obolibrary.org/report_queries/'
| |
|
| |
| [12:56] James Overton: And ROBOT reports can output in text, TSV, and HTML formats.
| |
|
| |
| [12:57] James Overton: Small HTML example: http://dashboard.obofoundry.org/dashboard/obi/robot_report.html
| |
|
| |
| [12:57] Sydney Cohen: okay thank you
| |
|
| |
| [13:01] Ugur Bayindir: Side question; the editor Anita was using looks neat, what was that? And do you suggest using it in daily ontology editing tasks?
| |
|
| |
| [13:03] Anita Caron: I agree.
| |
|
| |
| [13:01] Allen Baron: Looked like Microsoft VS code to me.
| |
|
| |
| [13:03] Anita Caron: I agree.
| |
|
| |
| [13:01] Allen Baron: …. and Protege for editing the ontology file itself.
| |
|
| |
| [13:08] Anita Caron: I agree.
| |
|
| |
| [13:02] Anita Caron: Hi Ugur, yes, I recommend using VS code in your daily ontology editing.
| |
|
| |
| [13:03] Ugur Bayindir: I agree.
| |
|
| |
| [13:02] Mike Bennett: My concern is that in such a deep dev environment, devs may write tests that only apply to application-focused ontologies (e.g. we saw redundant sub-class relations) which may not always be applicable to a concept ontology. Process needs to account for tests v stated style / aim of the ontology itself.
| |
|
| |
| [13:04] Nico Matentzoglu: Very good point Mike, I totally agree
| |
|
| |
| [13:05] Nico Matentzoglu: Customisability is key±
| |
|
| |
| [13:08] Allen Baron: What’s included the documentation ODK can automatically generate about an ontology?
| |
|
| |
| [13:11] Anita Caron: Complete tutorial for adding custom SPARQL check https://oboacademy.github.io/obook/tutorial/custom-qc/
| |
|
| |
| [13:12] C.M. Alvarez (USBP): I agree.
| |
|
| |
| [13:02] RaviSharma: James and Team today - great integration development and output effort.
| |
|
| |
| [13:05] James Overton: Yes, the editor Anita was using is VS Code.
| |
|
| |
| [13:11] RaviSharma: Thanks for informing that 40-70 users use this toolset and apps regularly.
| |
|
| |
| [13:19] James Overton: 40-70 ontology projects use ODK, that we know of. It's an open source project, so who knows how many people use it.
| |
|
| |
|
| == Resources == | | == Resources == |
| * [https://bit.ly/3YDzVIJ Video Recording]
| |
| * [https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]
| |
|
| |
|
| == Previous Meetings == | | == Previous Meetings == |
| {{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2023_02_08]] | | {{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2023_03_08]] |
| |?|?Session|mainlabel=-|order=desc|limit=3}} | | |?|?Session|mainlabel=-|order=desc|limit=3}} |
| | | |
| == Next Meetings == | | == Next Meetings == |
| {{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2023_02_08]] | | {{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2023_03_08]] |
| |?|?Session|mainlabel=-|order=asc|limit=3}} | | |?|?Session|mainlabel=-|order=asc|limit=3}} |
|
| |
|