Ontolog Forum

Session Track A Session 2
Duration 2 hour
Date/Time Apr 05 2017 18:30 GMT
9:30am PDT/12:30pm EDT
5:30pm BST/6:30pm CEST
Convener GaryBergCross

Ontology Summit 2017 Track A Session 2

Video Teleconference:

Meeting ID: 768423137

Chat room:

Please use the chatroom above. Do not use the video teleconference chat, which is only for communicating with the moderator.

When you use the Video Conference URL above, you will be given the choice of using the computer audio or using your own telephone. Some attendees had difficulties when using the computer audio choice. If this happens to you, please leave the meeting and reenter it using the telephone choice with access code 768423137.

Template:Blog:Session2 Automation of Ontology Development



[12:16] KenBaclawski:


Michael Yu (UCSD) "Inferring the hierarchical structure and function of a cell from millions of biological measurements".

Francesco Corcoglioniti (Post-doc at Fondazione Bruno Kessler, Italy) "Frame-based Ontology Population from text with PIKES"

Evangelos Pafilis (Hellenic Center Marine Research [HCMR]) EXTRACT 2.0: interactive extraction of environmental and biomedical contextual information."

[12:23] KenBaclawski: The video teleconference is at

[12:23] KenBaclawski: The meeting page is

[12:26] ToddSchneider: Ken, is the Blue Jeans recording capability working?

[12:30] KenBaclawski: @Todd: Yes, it is working. I have tried it, and it seems adequate.

[12:36] Rebecca Tauber: Does anybody know the meeting code for calling in? I'm having some connection trouble.

[12:37] gary berg-cross: @Rebecca does work???

[12:38] Rebecca Tauber: @Gary - finally got it to work, thanks (loading took forever)

[12:39] gary berg-cross: I have a bit of an echo...I am muted...

[12:40] ToddSchneider: Participants using Blue Jeans teleconference tool, please do not send video (i.e., don't use a/your web cam) to conserve bandwidth.

[12:41] ToddSchneider: Gary, I'm not hearing any echo.

[12:42] ToddSchneider: How does data acquisition impact any models created (e.g., implicit or embedded assumptions or biases)?

[12:44] ToddSchneider: What does the hierarchy represent?

[12:45] Rebecca Tauber: Are you pulling the public data from open-access articles, or curated data from databases?

[12:52] gary berg-cross: Reloaded to get rid of the echo.

[12:54] Mark Underwood: What tool was used for the visualization demo?

[12:59] Rebecca Tauber: May or may not be useful/relevant - have you looked into GIST (genetic interaction structured terminology)? Currently in development: (look at genetic interaction curation)

[13:01] ToddSchneider: What is a 'bundle' on interactions? Is there some additional behavior that emerges from a 'bundle' of interactions (i.e., is it another type of interaction)?

[13:05] ToddSchneider: Ken, There are more people listed on BlueJeans than on this chat.

[13:06] Mark Underwood: Is the "framework for supervised machine learning" a general design pattern, or something special that needs a deeper dive to apply to different domains?

[13:10] Mark Underwood: Is it ok to socialize the demonstration web page?

[13:12] Rebecca Tauber: Would love to see more about this project. I work on the Evidence & Conclusion Ontology and we work closely with GO.

[13:12] gary berg-cross: Francesco has a nice contrast or follow up from Valentina's FRED presentation.

[13:14] gary berg-cross: @Michael Yu, thanks for a nicely detailed presentation.

[13:15] Mark Underwood: @Michael 0 Nice presentation - and shout-out to San Diego (Long time former resident, Leucadia / La Mesa resident)

[13:16] KenBaclawski: @ToddSchneider: I will remind participants to join the soaphub chat during the break between speakers.

[13:21] AndreaWesterinen: @Francesco How do you get the correct parse of the Bush/Bono sentence to achieve the frame that you note in the slides? For example, "in Africa" could refer to where Bush and Bono are OR to the fight of HIV. Humans know that Bush and Bono are not in Africa, but a parser would not.

[13:21] Michael Yu: A 'bundle' of interactions is simply a dense cluster of interactions. In our experience, we find that bundles can occur in at least two ways. The first type of bundle spans BETWEEN two terms, i.e. there are many pairwise interactions (g1, g2) where g1 is in one term and g2 is in the other term. The second type of bundle occurs WITHIN a term, i.e. there are many interactions (g1,g2) where both g1 and g2 are in that same term. Bundling is a nice property because it means that many interactions can be more easily explained (and thus predicted) by that bundling

[13:23] gary berg-cross: Q from Queue for Francesco " Could you define the word Frame?"

[13:23] KenBaclawski: Please put your questions in the main entry box at the bottom. Do not put your question in the box next to the hand.

[13:27] Michael Yu: @RebeccaTauber. Thanks for the link about GIST! I will look into it.

Also, we have previously with GO (Mike Cherry, Michal A Surma, Rama Balakrishnan) by suggesting that they includes some data-driven terms into GO. See section "Using NeXO to systematically update and expand GO" of the Dutkowski et al. Nature Biotech 2012 paper (5th paper listed on slide 26). In general, I'm excited about merging data-driven and curated knowledge!

[13:31] Michael Yu: @MarkUnderwood. The visualization for was custom built. I believe it relies heavily on javascript libraries (Node.JS or related libraries I think?) More info can be found in the paper Dutkowski et al. Nucleic Acids Res 2014 (4th paper in slide 26)

[13:33] Michael Yu: @RebeccaTauber, the data used to create the ontology comes from both datasets tied to specific journal articles and also data that we downloaded from a database (e.g. we have used BioGRID database, which is described in the paper you linked)

[13:36] Michael Yu: @MarkUnderwood, sorry I'm not sure what you mean by "socialize" the demonstration web page

The supervised machine learning framework is a general method for creating informative features (a.k.a. "ontotype") to be used by any machine learning method, such as the decision trees I presented.

[13:38] Rebecca Tauber5: Thanks @Michael! It's great to see GO development being driven this way... really cool.

[13:40] gary berg-cross: I note that these text understanding efforts leverage ontologies like YAGO to provide background knowledge. This reflects our chicken and egg discussion last time that Track A and B views are intertwined in practice.

[13:41] gary berg-cross: Q from queue, " Again, what was the URL for PIKE?"

[13:45] ToddSchneider: Were the NLP tools 'tuned' or trained?

[13:51] gary berg-cross: @Francesco Thanks for a wonderful presentation with lots of work to build on.

[14:19] gary berg-cross: @Evangelos Thank you!

[14:31] Mark Underwood: yes, sorry, no audio here

[14:31] Mark Underwood: Yes, provide on Twitter etc

[14:32] Mark Underwood: Got it, thanks

[14:36] Mark Underwood: Thank you, presenters - very worthwhile


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