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Questions from Q & A
| Question | Questioner name | Answer | Panelist name |
|---|---|---|---|
| can you elaborate on which minimal information standards you are looking at? | mmiller@systemsbiology.org | The standards generated by this project are the ontologies guidelines, mapping tool requirements and mapping service requirements. These are all accessible through this public wiki. | |
Is the OM project considering SiLA/AnIML analytical and instrument data ontologies and standards? Can these be considered in Phase 3? Is the OM project primarily focused on experimental ontologies or also metadata of the instruments used for the data generation, being able to reference the instrument metadata for validation and experiment reproducibility | devon.johnston@sila-standard.com | Ontologies in the Disease and Phenotype domain are selected by the funders. However, the project guidelines are applicable to ontologies in any data domain. Likewise, mappings can found for any public ontologies hosted by EMBL-EBI, but their quality and value will not be assessed by Phase 3. | |
| How does these mappings interact with OMOP? Or is this a competitive view? | mmeighu@celgene.com | The Pistoia Alliance Ontologies Mapping project is open to collaboration with public organisations such as OHDSI, who provide the OMOP common data model. Mappings produced by Phase 3 will be shared on an openly available website such as through this public wiki at the appropriate time. | |
Roche is an EFPIA member of IMI1 (eTOX) and IMI2 (NexGETS). However, Martin didn't mention Roche's involvement which, in the case of eTOX, delivered the OntoBrowser which is designed to draw disparate terminologies together. Did Roche's 5-year involvement in this project have any impact on its Ontologies Mapping project and, if so, how? | philip.drew@pds-consultants.co.uk | ??? | |
For Martin and Yasmin ..where is the greatest value of using semantics - data ingestion, integration or consumption? | merchant_ron@lilly.com | ??? | |
In terms of diseases like cancer, where clinical ontologies vary from tumor type to tumor type how can one work on normalizing attributes in that case? | kundrar@mskcc.org | This is likely to benefit from collaboration with curators at the most relevant public ontology. Mapping between different source ontologies may also be part of the solution for building an application ontology. | |
| While ingesting a new data source, is there a prerequisite to have a data model / biz. model or ontology first? | merchant_ron@lilly.com | ??? | ??? |
| For SciBite -- your enrichment – are you adding content/ terms to HPO, MeSH directly? | jkranz@post.harvard.edu | Enrichment falls into 3 distinct areas: greater coverage for existing entities in ontologies, new entities in ontologies and new ontologies in spaces not served by the public domain (often very company specific). As much as possible we feedback to public sources for new entities as the value in having public IDs for these is of benefit to all. | |
For SciBite - how accurate are the ontology enrichments? What are the recall and precision pre- and post- enrichment? | peter.mcquilton@oerc.ox.ac.uk | This is a very difficult thing to measure. Obviously we have bio-creative for gene, disease and drug mainly. But even here if you take some of the top scoring open source tools and apply them to patents or internal documents you can get vastly different results. Further there are many ontologies and document types for which there is no published data. Thus, we rely on our users to evaluate precision/recall on a case by case basis, in their context as i think its the only way to see what happens in "real life" | Lee Harland |
Does the ontology driven search also cover clinical trials? Can we search on the basis of indication + targeted mutation (keeping combination mutations in mind) | kundrar@mskcc.org | That depends on the nature of the source data, but mining e.g. medline for clinical trials publication types and extracting out normalised mutations linked to indications is indeed something thats very straightforward to do (LH) | Lee Harland (Deactivated) |
For Simon: How do you distinguish between a sample based attribute and a patient based attribute? How do you connect the two? | kundrar@mskcc.org | ??? | Simon Jupp |
| Where is the greatest value of using semantics/ontologies .. unstructured, structured or semi-structured? | merchant_ron@lilly.com | I would say all 3. The act of combining structured + semi/unstructured data through common ontologies has great potential to power many different data analyses. This is why ontologies are so important, providing the semantic glue to connect all these (LH) | Lee Harland (Deactivated) |
Are there plans to aggregate OBO foundry and similars together with the ontologies hosted at EBI (AIM would be to have ontologies in "ONE" format and harmonized | matthias.negri@abbvie.com | ??? | Simon Jupp |
| what is the relationship between OLS and the other services and NCBO BioPortal out of Stanford, if any? | mmiller@systemsbiology.org | ??? | Simon Jupp |
| How is EMBL-EBI's OLS different from BioPortal ? | jkranz@post.harvard.edu | ??? | Simon Jupp |
How these EBI ontology tools compare to similar function BioPortal tools (such as annotation, ontology mapping)? Do the tools provide Rest API access? | jiezheng@upenn.edu | ??? | Simon Jupp |
For Lee - wonderful work being done at SciBite. Is there a plan to develop or integrate with cognitive processing such as IBM Watson? | monica.elrod@pfizer.com | I think this article (virtual-strategy.com/2016/12/06/why-semantics-data-linking-is-vital-to-artificial-intelligence/?utm_content=buffer44668&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer) describes the role of semantic data as a resource to power AI/ML processes. We see our work as providing substrate for input into any computing engine for whatever customers wish to do. Most of our collaborations are driven by real-world customer use cases. | |
| For Simon - will OXO be distributed for mirror installation? | william.spooner@eaglegenomics.com | ??? | Simon Jupp |
| How can we join this exciting community to knowledge share etc. | mmeighu@celgene.com | Contact Ian Harrow (Unlicensed) to join the Community of Interest | |
Real world things typically have different identifiers in different datasets - don't we also need co-reference resolution for actual data integration? | andreas.thalhammer@roche.com | Yes, absolutely. That could be one of the functions of an ontologies mapping service stored in a central database. | |
| How to apply mapped ontologies on non-English content? | s.tobaben@elsevier.com | Translate to a common language first, then apply mapping. |