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@hammer, I put together a [notebook](https://github.com/hammerlab/t-cell-relation-extraction/blob/04fe235bdbf78d3f5b93675a4ca13faea6e41500/pm_subtype_protein_relations/entity_linking/eda-word2vec.ipyn…
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Dear Omeed,
When running MTAG on the GWAS results of two related traits (UKB data, phenotypic correlation 0.6), with sample overlap, I picked up some loci that were not significant in the GWAS. Ho…
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From @cmungall : Only just saw this.
I would have said use the species specific proteins with IDs from uniprot
- clear SOP
- uniprot identifiers are well understood, no need for an additional l…
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If I'm not mistaken, the BrAPI studies can be used to represent phenotyping studies or genotyping studies (and maybe even other kinds in the future)
The problem is that for now there is no definite…
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this service call needs fixing:
http://monarchinitiative.org/phenome/Homo_sapiens.gff3
the score and strand order are reversed. this will require the monarch api to properly wrap the service call t…
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* All Trait and phenotype patterns have a modifier. This may be phenotype, trait or children of these terms.
* Modifier: normal/abnormal has parent class phenotype (?) This replaces deviation(from …
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```
HPO agrees with Bgee that fetus is post-embryo.
However, there are other disagreements:
* HP:0000004 ! Onset and clinical course
* HP:0003674 ! Onset [DEF: "The age and speed of the first a…
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currently we follow orphanet
```
is_a Orphanet:98053 ! Rare genetic disease
is_a Orphanet:183530 ! Rare genetic developmental defect during embryogenesis
is_a Orphanet:183536 ! Genet…
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It would be useful to have a module `ncit/subsets/abnormal-cell.owl`
This would contain the hierarchy under:
[NCIT:C12913](http://purl.obolibrary.org/obo/NCIT_C12913) ! Abnormal Cell
E.g.
…
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When I did run GAPIT with source("http://zzlab.net/GAPIT/gapit_functions.txt"), some models didn't make the results depending on the combinations of genotypic data and traits.
So I analysed the each …