maxo-annotation-ingest Report
The MAxO Annotation Ingest converts MAxO Annotation data to Biolink Model compliant KGX format.
Example annotation records:
| disease_id | disease_name | citation | maxo_id | maxo_label | hpo_id | maxo_relation | evidence_code | extension_id | extension_label | attribute | creator | last_update | created_on |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MONDO:0009797 | Orotic Aciduria | PMID:9042911 | MAXO:0010022 | uridine supplementation | MONDO:0009797 | TREATS | TAS | ORCID:0000-0002-0736-9199 | 2022-09-06 | 2022-09-06 | |||
| MONDO:0014590 | Myasthenic Syndrome, Congenital, 18 | PMID:25381298 | MAXO:0000434 | calcium channel blocking agent therapy | HP:0001324 | TREATS | TAS | CHEBI:51599 | 2,4-diaminopyridine | ORCID:0000-0002-0736-9199 | 2022-09-27 | 2022-09-27 | |
| MONDO:0014584 | Myasthenic Syndrome, Congenital, 3b, Fast-channel | PMID:11435464 | MAXO:0000210 | cholinesteriase inhibitor therapy | HP:0001324 | TREATS | TAS | CHEBI:8665 | Pyridostigmine | ORCID:0000-0002-0736-9199 | 2023-02-26 | 2023-02-26 | |
| MONDO:0010421 | Agammaglobulinemia, X-linked | PMID:26909497 | MAXO:0001480 | immunoglobulin infusion therapy | HP:0004432 | TREATS | PCS | ORCID:0000-0001-9969-9517 | 2023-06-10 | 2023-03-15 | |||
| MONDO:0010196 | Werner Syndrome | PMID:20301687 | MAXO:0001139 | calcium supplementation | HP:0000939 | PREVENTS | TAS | ORCID:0000-0002-4142-7153 | 2023-02-11 | 2022-02-28 | |||
| MONDO:0010156 | Spastic Paraplegia 20, Autosomal Recessive | PMID:20301556 | MAXO:0000011 | physical therapy | HP:0007340 | PREVENTS | TAS | ORCID:0000-0002-4142-7153 | 2022-02-28 | 2022-02-28 | |||
| MONDO:0008667 | Von Hippel-lindau Syndrome | PMID:20301636 | MAXO:0000058 | pharmacotherapy | HP:0009713 | PREVENTS | TAS | comment: "CHEBI:9513" | ORCID:0000-0002-4142-7153 | 2023-06-14 | 2022-08-01 | ||
| MONDO:0100079 | Epileptic Encephalopathy, Early Infantile, 6 (dravet Syndrome) | PMID:9596203 | MAXO:0000208 | sodium channel inhibitor therapy | HP:0032794 | CONTRAINDICATED | TAS | CHEBI:6367 | lamotrigine | comment: "Seizures can worsen on withdrawing lamotrigine." | ORCID:0000-0002-1735-8178 | 2023-07-12 | 2023-07-12 |
Mapping between MAxO relation and biolink predicate:
| maxo_relation | biolink_predicate |
|---|---|
| TREATS | biolink:ameliorates_condition |
| PREVENTS | biolink:prevantative_for_condition |
| CONTRAINDICATED | biolink:contraindicated_in |
The most straight forward transformation to biolink is when the medical action is related to the entire disease, in this instance, the hpo_id column will match the disease_id column.
| Field | Value |
|---|---|
| disease_id | MONDO:0009797 |
| disease_name | Orotic Aciduria |
| citation | PMID:9042911 |
| maxo_id | MAXO:0010022 |
| maxo_label | uridine supplementation |
| hpo_id | MONDO:0009797 |
| maxo_relation | TREATS |
| evidence_code | TAS |
| extension_id | |
| extension_label | |
| attribute | |
| creator | ORCID:0000-0002-0736-9199 |
| last_update | 2022-09-06 |
| created_on | 2022-09-06 |
This can be transformed into:
| Biolink Slot | Value |
|---|---|
| category | |
| subject | MAXO:0010022 |
| predicate | biolink:ameliorates_condition |
| object | MONDO:0009797 |
| publications | PMID:9042911 |
| agent | ORCID:0000-0002-0736-9199 |
| primary_knowledge_source | infores:maxo-annotations |
| aggregator_knowledge_source | infores:monarchinitiative |
| knowledge_level | knowledge_assertion |
| agent_type | manual_agent |
Edges Report
| category | subject_prefix | predicate | object_prefix | disease_context_qualifier_prefix | count |
|---|---|---|---|---|---|
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:ameliorates_condition | HP | MONDO | 744 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:ameliorates_condition | HP | OMIM | 2 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:ameliorates_condition | MONDO | MONDO | 40 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:contraindicated_in | HP | MONDO | 3 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:preventative_for_condition | HP | MONDO | 140 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:preventative_for_condition | MONDO | MONDO | 5 |
| biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation | MAXO | biolink:related_to | HP | MONDO | 17 |