https://github.com/monarch-initiative/mapping-walker
walks mapping graphs running boomer
https://github.com/monarch-initiative/mapping-walker
bioportal boomer entity-normalization knowledge-graphs mapping-commons mapping-tools mappings obofoundry ontologies ontology-lookup-service sssom
Last synced: 2 months ago
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walks mapping graphs running boomer
- Host: GitHub
- URL: https://github.com/monarch-initiative/mapping-walker
- Owner: monarch-initiative
- Created: 2022-03-19T00:38:23.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-05-24T23:55:23.000Z (almost 3 years ago)
- Last Synced: 2024-06-11T16:35:58.655Z (10 months ago)
- Topics: bioportal, boomer, entity-normalization, knowledge-graphs, mapping-commons, mapping-tools, mappings, obofoundry, ontologies, ontology-lookup-service, sssom
- Language: Python
- Homepage:
- Size: 1.7 MB
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Mapping Walker
This application will:
- crawl a mapping endpoint weaving a set of SSSOM mappings
- input these into boomer
- visualize the results with obographviz
__THIS IS ALPHA SOFTWARE__
## Requirements
You need the following on your path:
- [graphviz](https://graphviz.org/)
- [boomer](https://incatools.github.io/boomer/)
- [og2dot](https://github.com/cmungall/obographviz)
On MacOS you may need to install openblas via homebrew and set the `OPENBLAS` environment variable before installing dependencies:
```
brew install openblas
export OPENBLAS="$(brew --prefix openblas)"
poetry install
```
## Running
```bash
mapcrawl OMIM:603467
```
you can enter as many CURIEs as you like
The output looks like:
Note the visualization doesn't show the mappings that were rejected - see the full boomer report file. It shows things like:
- [Fanconi anemia](http://purl.obolibrary.org/obo/Orphanet_84) SiblingOf [OMIM_614087](http://purl.obolibrary.org/obo/OMIM_614087) 0.09999999999999998
- [Fanconi anemia](http://purl.obolibrary.org/obo/Orphanet_84) ProperSuperClassOf [OMIM_614087](http://purl.obolibrary.org/obo/OMIM_603467) (most probable) 0.8
- [aplastic anemia](http://purl.obolibrary.org/obo/MONDO_0015909) EquivalentTo [Anemia, Aplastic](http://purl.obolibrary.org/obo/MeSH_D000741) (most probable) 0.8
- [Fanconi anemia](http://purl.obolibrary.org/obo/DOID_13636) EquivalentTo [Fanconi Anemia](http://purl.obolibrary.org/obo/MeSH_D005199) (most probable) 0.8
## Gallery
### Anatomy
* FMA:24879
these are the full results:
- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) EquivalentTo [Lower Extremity](http://purl.obolibrary.org/obo/MeSH_D035002) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/UMLS_C1522391) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/XAO_0003031) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/BTO_0002345) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) SiblingOf [](http://purl.obolibrary.org/obo/NCIT_C77625) 0.09999999999999998
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/MeSH_D006614) (most probable) 0.8
- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) SiblingOf [](http://purl.obolibrary.org/obo/NCIT_C12742) 0.09999999999999998
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C12742) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) SiblingOf [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) 0.09999999999999998
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/XAO_0003031) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [obsolete_hindlimb](http://purl.obolibrary.org/obo/EFO_0000883) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/EMAPA_17458) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Free lower limb](http://purl.obolibrary.org/obo/FMA_24879) (most probable) 0.8
- [Hindlimb](http://purl.obolibrary.org/obo/UMLS_C1522391) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/MeSH_D006614) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [lower limb](http://purl.obolibrary.org/obo/EHDAA2_0001033) (most probable) 0.8
- [leg](http://purl.obolibrary.org/obo/UBERON_0000978) EquivalentTo [Lower Extremity](http://purl.obolibrary.org/obo/MeSH_D035002) (most probable) 0.8
- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C77625) (most probable) 0.8
- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/MA_0000026) (most probable) 0.8
note boomer effectively rejected some links (SiblingOf) that came from some mappings
### Disease
MONDO:0019249 ! mucopolysaccharidosis
## How it works
It currently queries OxO - it will do a breadth first search until either saturated or either max depth or max queries is reached
All configuration is specified in LinkML yaml - docs will be up soon
Currently it applies the standard SSSOM-py mappings for all predicates obtained from OxO (most mappings in OxO are RELATED but there are some narrow/broad)
Default confidence is 0.8 (currently no mappings in OxO have confidence)
We don't yet allow plugin in of rules - e.g. boost confidence if mapping comes from a more trusted source, or is HumanCurated
## TODO
- fix CURIEs
- add bioportal endpoint (currently uses oxo)
- add ubergraph endpoint