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Phenotype comparison tools using semantic similarity.

License: Other

Dockerfile 0.65% Python 99.35%

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carlosborroto 382982408 deepsystemspharmacology geng-lee xen-biomed arvkevi emmanuelgonz krttrr rebeccaito jessime

phenopy's Issues

Add w2v binary

Hey @vgainullin, can you add the w2v binary to the phenoseries branch?

incorrect downloads path

020-03-04 01:40:59,906 - phenopy - INFO - Incorrect url specified for HPO files: http://compbio.charite.de/jenkins/job/hpo.annotations.current/lastSuccessfulBuild/artifact/misc_2018/phenotype.hpoa

Does nx.ancestors return children or ancestors?

    # compile list of HPO terms to include in the calculation, term plus children
    hpo_id_plus_children = [hpo_id] + list(nx.ancestors(hpo_network, hpo_id))

Related to this, what would the impact be of taking only immediate children rather than all children? That is, are we giving too much IC to less specific terms with this method?

Calculate gene similarity on the HPO

Dear Kevin,

I would like to calculate the similarity for a few genes (~2000).
I annotated these genes with the HPO codes from the human phenotype ontology webpage (http://compbio.charite.de/jenkins/job/hpo.annotations/lastSuccessfulBuild/artifact/util/annotation/genes_to_phenotype.txt).

I obtained reshaped and got a file like this:

A4GALT	.	HP:0010970|HP:0000006
AAAS	.	HP:0040281|HP:0040282|HP:0040283|HP:0011463|HP:0001278|HP:0000972|HP:0012332|HP:0008259|HP:0004322|HP:0001251|HP:0000648|HP:0000007|HP:0002571|HP:0004319|HP:0001263|HP:0008163|HP:0001249|HP:0009916|HP:0003487|HP:0007002|HP:0000252|HP:0001347|HP:0000522|HP:0003676|HP:0000649|HP:0001324|HP:0000953|HP:0001260|HP:0000846|HP:0001250|HP:0007440|HP:0000505|HP:0000982|HP:0001761|HP:0010486|HP:0000830|HP:0007556|HP:0002093|HP:0001430|HP:0001252|HP:0002376|HP:0000612|HP:0000407
AASS	.	HP:0000119|HP:0000752|HP:0001083|HP:0001903|HP:0003593|HP:0001250|HP:0002161|HP:0000736|HP:0001252|HP:0100543|HP:0000007|HP:0001256|HP:0000750|HP:0001249
ABAT	.	HP:0025356|HP:0000278|HP:0000098|HP:0007291|HP:0000007|HP:0002415|HP:0001321|HP:0000494|HP:0001347|HP:0006829|HP:0001263|HP:0001274|HP:0001250|HP:0001254|HP:0025430|HP:0003819
ABCA4	.	HP:0040280|HP:0040281|HP:0040282|HP:0040283|HP:0040284|HP:0000006|HP:0007663|HP:0000662|HP:0001133|HP:0000608|HP:0000512|HP:0000543|HP:0000007|HP:0007737|HP:0007722|HP:0000510|HP:0007984|HP:0007843|HP:0000548|HP:0000580|HP:0000572|HP:0008035|HP:0000639|HP:0000618|HP:0000405|HP:0000603|HP:0000135|HP:0000493|HP:0000463|HP:0001249|HP:0007703|HP:0000613|HP:0000987|HP:0030329|HP:0000649|HP:0000648|HP:0000551|HP:0008046|HP:0000407|HP:0007704|HP:0007814|HP:0008736|HP:0000035|HP:0008002|HP:0007675|HP:0000431|HP:0000610|HP:0000518|HP:0000602|HP:0001513|HP:0008059|HP:0000501|HP:0000563|HP:0000842|HP:0030500|HP:0001347|HP:0000505|HP:0005978|HP:0011504|HP:0011462|HP:0011463|HP:0003621|HP:0007994
ABCB11	.	HP:0040283|HP:0000989|HP:0002014|HP:0003155|HP:0000952|HP:0001081|HP:0003593|HP:0001394|HP:0001744|HP:0001046|HP:0002240|HP:0002630|HP:0002908|HP:0000007|HP:0003819|HP:0004322|HP:0001508|HP:0001406|HP:0001402

which I think is the correct format for phenopy. I then used the command:

phenopy score gene_lists_with_HPO.txt --threads 12 --self

and I got as output something like this:

#query	entity_id	score
A4GALT	A4GALT	1.0
A4GALT	ABCD1	0.0
A4GALT	ACAT1	0.010405043493187662
A4GALT	ACVRL1	0.03336405048957507
A4GALT	ADGRG1	0.0
A4GALT	AGXT	0.009234121604447244
A4GALT	AKT1	0.003509945769583653
A4GALT	ALG1	0.0
A4GALT	AMER1	0.0

However, the identity for some genes are not 1 as I was expecting. For instance:

ABCB7 ABCB7 0.5558528984777618

Would you expect something like this? How would you explain it?
Should I use a different --summarization-method ?

Best regards,

Luca

remove rounding

We should be returning the full float.

install error

fresh install from pip results in

FileNotFoundError: [Errno 2] No such file or directory: '/miniconda3/lib/python3.7/site-packages/phenopy/data/phenopy.wv.model.txt.gz'

add simreg as a similarity metric

https://cran.r-project.org/package=SimReg

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827100/

should we add this as a similarity metric?

Incorrect url specified for HPO files

http://compbio.charite.de/jenkins/job/hpo.annotations.current/lastStableBuild/artifact/current/phenotype.hpoa
does not exist

https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/
should be used instead?

update code that uses networkx

G.node has been removed from the library in 2.4 and should be refactored here.

Errors (and solutions) with anaconda on Windows 10

Hello,

Thank you for the package.

Two issues when trying to use this in anaconda on Windows 10:

the pip package is outdated and does not (yet) have the score_term_sets_basic function mentioned in the readme as an example. Of course cloning from git solves this.
this line


config_directory = os.path.join(os.environ.get('HOME'), f'.{__project__}')

will give an error and should be changed to


config_directory = os.path.join(os.environ.get('CONDA_PREFIX'), f'.{__project__}')

Hope this helps other people!

Many thanks

update parser for phenotype.hpoa

HPO added a "#" to the header line with column names in the phenotype.hpoa file.

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