More generally: I'm becoming aware of other efforts to annotate relevant texts, either the CORD-19 corpus, or supersets (e.g general coronavirus literature). Is anyone aware of any attempts to loosely coordinate these efforts? It would be great to have a resource for people to download all text annotations in a single format combining annotations from groups specializing in NER vs relation extraction, clinical markup vs omics markup, ... On Fri, Mar 20, 2020 at 10:11 AM Chris Mungall <cjmungall@lbl.gov> wrote: > This looks great! > > Is there a dummies guide on how to use this? > > It looks like there is a FHIR datamodel for modeling textual spans and you > are using this to represent the results of NER. What NER tool was used? > > It looks like snomed was the main vocabulary used - this makes sense for > marking up conditions, medications, and procedures. But what about genes > (human and viral), mechanisms (e.g. viral gene function) - do you plan to > run this with any OBO ontologies? > > On Thu, Mar 19, 2020 at 8:44 PM Jiang, Guoqian, M.D., Ph.D. < > Jiang.Guoqian@mayo.edu> wrote: > >> >> We are pleased to announce an initial version of the CORD-19-on-FHIR >> >dataset for COVID-19 research, a dataset of 13202 journal articles >> >relevant to novel coronavirus research. This dataset extends the >> >CORD-19 dataset (on which it is based) by adding several semantic >> >annotations. It is represented in FHIR RDF to facilitate semantic >> >linkage with other biomedical datasets. >> > >> >CORD-19-on-FHIR dataset currently adds the following semantic >> annotations: >> > >> >- Conditions: 103,968 instances >> >- Medications: 16,406 instances >> >- Procedures: 54,720 instances >> > >> >CORD-19-on-FHIR is available on github, and collaboration is invited: >> >https://github.com/fhircat/CORD-19-on-FHIR >> > >> >It is licensed to encourage open COVID-19 research. See specific terms: >> >https://github.com/fhircat/CORD-19-on-FHIR/blob/master/LICENSE >> > >> >CORD-19-on-FHIR was funded by the FHIRCat research grant, which seeks to >> >enable the semantics of FHIR and terminologies for clinical and >> >translational research: >> >https://github.com/fhircat/FHIRCat >> > >> >Sincerely, >> >> >Guoqian Jiang (Mayo Clinic), Harold Solbrig (Johns Hopkins University), >> >and FHIRCat team >> >> >>
Received on Friday, 20 March 2020 17:17:36 UTC