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Hello,
I was running a document through OGER for NER using [Human Phenotype Ontology (HP)](http://obofoundry.org/ontology/hp.html). The document contained the phrase "restrictive deficit on pulmona…
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Issue what I noticed:
During target cohort creation log says:
>2021-07-08 12:35:11 [Main thread] INFO PioneerWatchfulWaiting instantiateCohortSet 20/70: Instantiation cohort [PIONEER T5a] Symptom …
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**HPO term**
https://hpo.jax.org/app/browse/term/HP:0025419
**Suggested revision of textual definition**
A pneumatocele is a thin walled, gas-filled space in the lung. It is most frequently cause…
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We're using `oboInOwl:hasDbXref` relationships to translate information from other terminologies into EFO terms.
There are a few easy-to-detect xref values that are likely invalid. I imagine xrefs …
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# Basic task
Create a JSON document in this repository called PFT-example.json. The JSON should roughly model out what a PFT could look like if it was a [DiagnosticReport](https://www.hl7.org/fhir/…
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**Preferred term label:** Pulmonary nodule
**Synonyms**
**Definition (free text, please give PubMed ID)**
Focal rounded or ovoid opacity, ≤ 3 cm in diamter
**Parent term (use hpo.jax.o…
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https://github.com/NCATSTranslator/testing/issues/55 issues a [multi-hop query](https://github.com/NCATSTranslator/testing/blob/main/ars-requests/not-none/sharedPhenotypes.json). In the [BTE results](…
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**Preferred term label:** Septic pulmonary emboli
**Synonyms**
**Definition (free text, please give PubMed ID)**
Embolisation of intravascular thrombus containing microorganisms into the lung…
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We should use the Fleisher definition for this term?
https://hpo.jax.org/app/browse/term/HP:0025175
Honeycombing represents destroyed and fibrotic lung tissue containing numerous cystic airspace…
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https://codelists.opensafely.org/codelist/user/richard-croker/chronic-obstructive-pulmonary-disease-copd-annual-review/410dd25f/
As per the asthma annual review - only "annual review" codes include…