monarch-initiative/mapping-walker

walks mapping graphs running boomer

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
• boomer
• og2dot

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

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 SiblingOf OMIM_614087 0.09999999999999998
• Fanconi anemia ProperSuperClassOf OMIM_614087 (most probable) 0.8
• aplastic anemia EquivalentTo Anemia, Aplastic (most probable) 0.8
• Fanconi anemia EquivalentTo Fanconi Anemia (most probable) 0.8

Gallery

Anatomy

• FMA:24879

these are the full results:

• Lower Extremity EquivalentTo Lower Extremity (most probable) 0.8
• hindlimb EquivalentTo Hindlimb (most probable) 0.8
• hindlimb EquivalentTo hindlimb (most probable) 0.8
• hindlimb EquivalentTo hindlimb (most probable) 0.8
• hindlimb SiblingOf 0.09999999999999998
• hindlimb EquivalentTo Hindlimb (most probable) 0.8
• Lower Extremity SiblingOf 0.09999999999999998
• hindlimb EquivalentTo (most probable) 0.8
• hindlimb SiblingOf Lower Extremity 0.09999999999999998
• hindlimb EquivalentTo hindlimb (most probable) 0.8
• hindlimb EquivalentTo obsolete_hindlimb (most probable) 0.8
• hindlimb EquivalentTo hindlimb (most probable) 0.8
• hindlimb EquivalentTo Free lower limb (most probable) 0.8
• Hindlimb EquivalentTo Hindlimb (most probable) 0.8
• hindlimb EquivalentTo lower limb (most probable) 0.8
• leg EquivalentTo Lower Extremity (most probable) 0.8
• Lower Extremity EquivalentTo (most probable) 0.8
• hindlimb EquivalentTo hindlimb (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

mapping-walker's Issues

add bioportal endpoint

this would involve essentially making a parallel implementation of OxoWalker here: https://github.com/cmungall/mapping-walker/blob/main/src/mapping_walker/walkers/endpoints.py

PMID filter

should OxO really return PMIDs as mappings? maybe this is an upstream OBO problem. cc @matentzn

- [rough endoplasmic reticulum](http://purl.obolibrary.org/obo/PLANA_0007514) SiblingOf [](http://purl.obolibrary.org/obo/PMID_30143032)                0.09999999999999998
- [gamma neoblast](http://purl.obolibrary.org/obo/PLANA_0000039) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27013241)             0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27013241)             0.09999999999999998
- [neuropil](http://purl.obolibrary.org/obo/PLANA_0000470) SiblingOf [](http://purl.obolibrary.org/obo/PMID_29291981)           0.09999999999999998
- [neoblast](http://purl.obolibrary.org/obo/PLANA_0000429) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19174194)           0.09999999999999998
- [muscle cell](http://purl.obolibrary.org/obo/PLANA_0000101) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27063937)                0.09999999999999998
- [Neurons](http://purl.obolibrary.org/obo/UMLS_C0027882) EquivalentTo [Neurons](http://purl.obolibrary.org/obo/MeSH_D009474)   (most probable) 0.8
- [dopaminergic neuron](http://purl.obolibrary.org/obo/PLANA_0000482) SiblingOf [](http://purl.obolibrary.org/obo/PMID_23903188)                0.09999999999999998
- [pharynx](http://purl.obolibrary.org/obo/PLANA_0000016) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27163480)            0.09999999999999998
- [clonogenic neoblast](http://purl.obolibrary.org/obo/PLANA_0000046) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27150006)                0.09999999999999998
- [GABAergic neuron](http://purl.obolibrary.org/obo/PLANA_0000464) SiblingOf [](http://purl.obolibrary.org/obo/PMID_29291981)           0.09999999999999998
- [neuron](http://purl.obolibrary.org/obo/PLANA_0000099) SiblingOf [](http://purl.obolibrary.org/obo/PMID_24040508)             0.09999999999999998
- [renal system](http://purl.obolibrary.org/obo/PLANA_0000088) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19048075)               0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27063937)             0.09999999999999998
- [body wall musculature](http://purl.obolibrary.org/obo/PLANA_0000240) SiblingOf [](http://purl.obolibrary.org/obo/PMID_19174194)              0.09999999999999998
- [central nervous system](http://purl.obolibrary.org/obo/PLANA_0000103) EquivalentTo [](http://purl.obolibrary.org/obo/PMID_29291981)  (most probable) 0.8
- [vitelline gland](http://purl.obolibrary.org/obo/PLANA_0000231) SiblingOf [](http://purl.obolibrary.org/obo/PMID_27163480)            0.09999999999999998
- [neuron](http://purl.obolibrary.org/obo/CL_0000540) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C12623)       (most probable) 0.8

create a simple UI

Use OAK for endpoint access

Replace endpoints.py with using oak

test this with different providers:

ols, bioportal, local ontology file