import orthology data from AGR

[andrewsu]

The Alliance of Genome Resources (AGR) is a consortium of the most highly-used model organisms (mouse, rat, worm, fly, zebrafish, yeast), and they have released their own set of ortholog assignments at https://www.alliancegenome.org/downloads#orthology. Currently we have homologene in mygene.info, but I think this AGR set would be considered much more reliable for the organisms listed.

[NikkiBytes]

The parser and manifest repo is here . A few tests queries can be found in this notebook.

The repo was passed along for final deployment into mygene API, will update status when it is available.

[zcqian]

Commits imported, see https://github.com/biothings/mygene.info/commit/360b97162dcb16eb4f4eb4e1e73e278b9045dcf4 and the commits prior to this one. Subject of each commit has been prepended with the text "orthologyAGR:". Will close the issue after successfully running and importing the data into the builds.

[zcqian]

Hi @NikkiBytes Can you add metadata to the plugin so that it correctly reports the origin and license of the data?

You can see how it's done here and here

[NikkiBytes]

@zcqian it's added!

[zcqian]

@NikkiBytes I see that you modified setup_release in parser.py as well. Is this change also intended?

Also, you can fork this repository and open a pull request next time, it's easier to merge the changes that way. I can just incorporate the changes from your repository into this repository this time.

[NikkiBytes]

A few updates....

The document structure has been updated, example output below:

[
    {
        "_id": "176377",
        "agr": {
            "ortholog": [
                {
                    "geneid": "SGD:S000003566",
                    "symbol": "VPS53",
                    "taxid": "NCBITaxon:559292",
                    "algorithmsmatch": 9,
                    "outofalgorithms": 10,
                    "isbestscore": true,
                    "isbestrevscore": true
                }
            ]
        }
    },
    {
        "_id": "ZDB-GENE-041114-199",
        "agr": {
            "ortholog": [
                {
                    "geneid": "SGD:S000003566",
                    "symbol": "VPS53",
                    "taxid": "NCBITaxon:559292",
                    "algorithmsmatch": 8,
                    "outofalgorithms": 10,
                    "isbestscore": true,
                    "isbestrevscore": true
                }
            ]
        }
    },
    {
        "_id": "1311391",
        "agr": {
            "ortholog": [
                {
                    "geneid": "SGD:S000003566",
                    "symbol": "VPS53",
                    "taxid": "NCBITaxon:559292",
                    "algorithmsmatch": 7,
                    "outofalgorithms": 9,
                    "isbestscore": true,
                    "isbestrevscore": true
                }
            ]
        }
    }
.
.
.
]

Notes:

• The variable, "algorithms": "PhylomeDB|OrthoFinder|Hieranoid|OMA|Ensembl Compara|Roundup|InParanoid|PANTHER|OrthoInspector" is available in the data file. Currently the created output document doesn't include it (as shown above), but it can easily be added. [Note, if it is added, @newgene and I discussed possibly reformatting the data string into a list.] I noted this also in the README.md file in the repository.
  i.e. "PhylomeDB|OrthoFinder|Hieranoid|OMA|Ensembl Compara|Roundup|InParanoid|PANTHER|OrthoInspector" ---> ["PhylomeDB", "OrthoFinder", "Hieranoid", "OMA", "Ensembl", "Compara", "Roundup", "InParanoid", "PANTHER", "OrthoInspector"]

• There are some gene _id variables that are returning None when querying with biothings_client. You can see it in the example above, the second document "_id": "ZDB-GENE-041114-199" returned None when querying with these commands.....

from biothings_client import get_client

gene_client = get_client('gene')

gene=gene_client.getgene(gene_id, fields='symbol,name')

Maybe there is another query method I can use, or there will be unique ID cases without matches? @newgene @andrewsu

[zcqian]

Can you add a mapping document to the plugin? Thanks!

[newgene]

@NikkiBytes let's make the taxid field as an integer.

[zcqian]

@NikkiBytes I assume you're done making the changes at https://github.com/NikkiBytes/orthologyAGR ? If so I will merge the changes

[newgene]

added @jal347 to work with @NikkiBytes on the deployment on mygene.info API.