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Add new source to various places
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@bgyori
bgyori committed Jul 23, 2024
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39 changes: 20 additions & 19 deletions README.md
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Expand Up @@ -67,25 +67,26 @@ Reading systems:

Biological pathway databases:

| Database / Exchange format | Module | Reference |
|----------------------------|----------------------------|-----------------------------------------------------------------|
| PathwayCommons / BioPax | [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html) | http://pathwaycommons.org/ <br/> http://www.biopax.org/ |
| Large Corpus / BEL | [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html) | https://github.com/pybel/pybel <br/> https://github.com/OpenBEL |
| Signor | [`indra.sources.signor`](https://indra.readthedocs.io/en/latest/modules/sources/signor/index.html) | https://signor.uniroma2.it/ |
| BioGRID | [`indra.sources.biogrid`](https://indra.readthedocs.io/en/latest/modules/sources/biogrid/index.html) | https://thebiogrid.org/ |
| Target Affinity Spectrum | [`indra.sources.tas`](https://indra.readthedocs.io/en/latest/modules/sources/tas/index.html#) | https://doi.org/10.1101/358978 |
| HPRD | [`indra.sources.hprd`](https://indra.readthedocs.io/en/latest/modules/sources/hprd/index.html) | http://www.hprd.org | |
| TRRUST | [`indra.sources.trrust`](https://indra.readthedocs.io/en/latest/modules/sources/trrust.html) | https://www.grnpedia.org/trrust/ | |
| Phospho.ELM | [`indra.sources.phosphoelm`](https://indra.readthedocs.io/en/latest/modules/sources/phosphoelm/index.html) | http://phospho.elm.eu.org/ |
| VirHostNet | [`indra.sources.virhostnet`](https://indra.readthedocs.io/en/latest/modules/sources/virhostnet/index.html) | http://virhostnet.prabi.fr/ |
| CTD | [`indra.sources.ctd`](https://indra.readthedocs.io/en/latest/modules/sources/ctd/index.html) | http://ctdbase.org |
| DrugBank | [`indra.sources.drugbank`](https://indra.readthedocs.io/en/latest/modules/sources/drugbank/index.html) | https://www.drugbank.ca/ |
| OmniPath | [`indra.sources.omnipath`](https://indra.readthedocs.io/en/latest/modules/sources/omnipath/index.html) | https://omnipathdb.org/ |
| DGI | [`indra.sources.dgi`](https://indra.readthedocs.io/en/latest/modules/sources/dgi/index.html) | https://www.dgidb.org/ |
| CRoG | [`indra.sources.crog`](https://indra.readthedocs.io/en/latest/modules/sources/crog/index.html) | https://github.com/chemical-roles/chemical-roles |
| CREEDS | [`indra.sources.creeds`](https://indra.readthedocs.io/en/latest/modules/sources/creeds/index.html) | https://maayanlab.cloud/CREEDS/ |
| UbiBrowser | [`indra.sources.ubibrowser`](https://indra.readthedocs.io/en/latest/modules/sources/ubibrowser.html) | http://ubibrowser.ncpsb.org.cn/ |
| ACSN | [`indra.sources.acsn`](https://indra.readthedocs.io/en/latest/modules/sources/acsn.html) | https://acsn.curie.fr/ACSN2/ACSN2.html |
| Database / Exchange format | Module | Reference |
|----------------------------|------------------------------------------------------------------------------------------------------------|---------------------------|
| PathwayCommons / BioPax | [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html) | http://pathwaycommons.org/ <br/> http://www.biopax.org/ |
| Large Corpus / BEL | [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html) | https://github.com/pybel/pybel <br/> https://github.com/OpenBEL |
| Signor | [`indra.sources.signor`](https://indra.readthedocs.io/en/latest/modules/sources/signor/index.html) | https://signor.uniroma2.it/ |
| BioGRID | [`indra.sources.biogrid`](https://indra.readthedocs.io/en/latest/modules/sources/biogrid/index.html) | https://thebiogrid.org/ |
| Target Affinity Spectrum | [`indra.sources.tas`](https://indra.readthedocs.io/en/latest/modules/sources/tas/index.html#) | https://doi.org/10.1101/358978 |
| HPRD | [`indra.sources.hprd`](https://indra.readthedocs.io/en/latest/modules/sources/hprd/index.html) | http://www.hprd.org | |
| TRRUST | [`indra.sources.trrust`](https://indra.readthedocs.io/en/latest/modules/sources/trrust.html) | https://www.grnpedia.org/trrust/ | |
| Phospho.ELM | [`indra.sources.phosphoelm`](https://indra.readthedocs.io/en/latest/modules/sources/phosphoelm/index.html) | http://phospho.elm.eu.org/ |
| VirHostNet | [`indra.sources.virhostnet`](https://indra.readthedocs.io/en/latest/modules/sources/virhostnet/index.html) | http://virhostnet.prabi.fr/ |
| CTD | [`indra.sources.ctd`](https://indra.readthedocs.io/en/latest/modules/sources/ctd/index.html) | http://ctdbase.org |
| DrugBank | [`indra.sources.drugbank`](https://indra.readthedocs.io/en/latest/modules/sources/drugbank/index.html) | https://www.drugbank.ca/ |
| OmniPath | [`indra.sources.omnipath`](https://indra.readthedocs.io/en/latest/modules/sources/omnipath/index.html) | https://omnipathdb.org/ |
| DGI | [`indra.sources.dgi`](https://indra.readthedocs.io/en/latest/modules/sources/dgi/index.html) | https://www.dgidb.org/ |
| CRoG | [`indra.sources.crog`](https://indra.readthedocs.io/en/latest/modules/sources/crog/index.html) | https://github.com/chemical-roles/chemical-roles |
| CREEDS | [`indra.sources.creeds`](https://indra.readthedocs.io/en/latest/modules/sources/creeds/index.html) | https://maayanlab.cloud/CREEDS/ |
| UbiBrowser | [`indra.sources.ubibrowser`](https://indra.readthedocs.io/en/latest/modules/sources/ubibrowser.html) | http://ubibrowser.ncpsb.org.cn/ |
| ACSN | [`indra.sources.acsn`](https://indra.readthedocs.io/en/latest/modules/sources/acsn.html) | https://acsn.curie.fr/ACSN2/ACSN2.html |
| STK Atlas | [`indra.sources.stk_atlas`](https://indra.readthedocs.io/en/latest/modules/sources/stk_atlas.html) | https://www.nature.com/articles/s41586-022-05575-3 |

Custom knowledge bases:

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1 change: 1 addition & 0 deletions doc/modules/sources/index.rst
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Expand Up @@ -39,6 +39,7 @@ Molecular Pathway Databases
omnipath/index
ubibrowser
acsn
stk_atlas

Chemical Information Databases
------------------------------
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6 changes: 4 additions & 2 deletions indra/resources/default_belief_probs.json
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Expand Up @@ -34,7 +34,8 @@
"creeds": 0.01,
"ubibrowser": 0.01,
"acsn": 0.01,
"semrep": 0.05
"semrep": 0.05,
"stkatlas": 0.05
},
"rand": {
"eidos": 0.3,
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"creeds": 0.1,
"ubibrowser": 0.1,
"acsn": 0.1,
"semrep": 0.3
"semrep": 0.3,
"stkatlas": 0.3
}
}
10 changes: 10 additions & 0 deletions indra/resources/source_info.json
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Expand Up @@ -328,5 +328,15 @@
"color": "white",
"background-color": "#bf98eb"
}
},
"stkatlas": {
"name": "STK Atlas",
"link": "https://www.nature.com/articles/s41586-022-05575-3",
"type": "database",
"domain": "biology",
"default_style": {
"color": "white",
"background-color": "#ffa07a"
}
}
}
2 changes: 1 addition & 1 deletion indra/util/statement_presentation.py
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Expand Up @@ -121,7 +121,7 @@ class to define a `StmtStat`.
db_sources = ['psp', 'cbn', 'pc', 'bel_lc', 'signor', 'biogrid',
'tas', 'hprd', 'trrust', 'ctd', 'vhn', 'pe', 'drugbank',
'omnipath', 'conib', 'crog', 'dgi', 'minerva', 'creeds',
'ubibrowser', 'acsn']
'ubibrowser', 'acsn', 'stk_atlas']
"""Database source names as they appear in the DB"""

reader_sources = ['geneways', 'tees', 'gnbr', 'semrep', 'isi', 'trips',
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