ielis / hpo-toolkit Goto Github PK

Separate traversal from augmentation to remove include_source attribute on the relevant OntologyGraph methods.

We should not export SimpleHpoDiseaseAnnotation, SimpleHpoDisease, and SimpleHpoDiseases from hpotk.annotations module.

It would be nice to have a convenience function for loading the hpo that would look if the HPO is already downloaded and if not pull in the latest version from GitHub, i.e., internally it would do somethinglike this

if os.path.isfile('hpo_data/hp.json'):
    hpo_ontology = load_ontology('hpo_data/hp.json')
else:
    hpo_ontology = load_ontology('https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.json')

and client code would look like this

load_ontology()
# or if you want to make sure you have the latest version
load_ontology(overwrite=True)

Is there a way to get synonyms of terms using the HPO ID?

Hi,

I have just stumbled upon your hpo-toolkit library and see that it has some very nice features. I have been working on a similar library, which is already quite stable, extendable and very well tested: PyHPO (Docs). I was wondering if you think it would make sense to combine our efforts and work on one library together.

It would be useful to be able to get PMIDs that go with term definitions. In the JSON file these are listed as

 {
      "id" : "http://purl.obolibrary.org/obo/HP_0000011",
      "lbl" : "Neurogenic bladder",
      "type" : "CLASS",
      "meta" : {
        "definition" : {
          "val" : "A type of bladder dysfunction caused by neurologic damage. Neurogenic bladder can be flaccid or spastic. Com
mon manifestatios of neurogenic bladder are overflow incontinence, frequency, urgency, urge incontinence, and retention.",
          "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:18095004", "PMID:22400020" ]
        },
(...)

There are different ways we could model this in HPOTK; I do not think it is necessary to make them explicitly part of the definition, but they could be or each term could get a list of PMID_xref or something like that?