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Changes in EpiGraphDB v1.0

Here we document the changes regarding the EpiGraphDB platform and database from version 0.3 (2020-04) to version 1.0 (2021-03).

Overall architecture and components

  • There is a major overhaul in the data integration pipeline and is now open sourced as epigraphdb-graph.

Schema and entity representation

General changes

  • meta properties: each meta entity contains the following meta properties,
    • _id: unique id
    • _name: human readable label
    • _source: data source(s) of the entity

Meta nodes

  • Meta: We have dropped the use of a Meta node for metadata information.
  • Disease
  • Drug
  • Efo
  • Event: Removed due to overhaul of source Reactome
  • Gene
    • new props: biomart_source
  • Gwas
    • new props: build
  • Literature
    • new props: doi
    • renamed props:
      • pubmid_id: id
  • Pathway
    • removed props: in_disease
    • renamed props:
      • reactome_id: id
  • Protein
    • new props: name
  • SemmedTriple: Renamed to LiteratureTriple. Entity labels are now removed from LiteratureTriples and only CUI id remain. Users will need to match from LiteratureTerm to get the entity labels.
    • removed props: count, subject_name, object_name, subject_type, object_type
    • new props: name (merge subject_name, predicate, object_name together)
  • SemmedTerm: Renamed to LiteratureTerm
    • removed props: count
  • Tissue
    • renamed props: tissue: {id, name}
  • Variant
    • new props: pos, chr, ref, alt, build

Meta rels

  • BN_GEN_COR: Renamed to GEN_COR
    • renamed props:
      • se: rg_SE
      • z: Z
      • h2_int: h2_intercept
      • h2_int_se: h2_intercept_SE
    • new props: rpheno, rg_intercept, rg_intercept_SE
    • removed props
      • h2_obs, h2_obs_se
      • gcov_int, gcov_int_se
  • CPIC
  • EFO_CHILD_OF
  • EVENT_IN_PATHWAY: Removed due to overhauled source Reactome
  • EXPRESSED_IN
  • GENE_TO_LITERATURE: Removed due to overhauled source Reactome
  • GENE_TO_PROTEIN
  • GWAS_NLP
  • GWAS_NLP_EFO
  • GWAS_SEM: Renamed to GWAS_TO_LITERATURE_TRIPLE
  • GWAS_TO_LIT: Renamed to GWAS_TO_LITERATURE
  • GWAS_TO_VARIANT
  • INTACT_INTERACTS_WITH_GENE_GENE: Removed due to obsolete source IntACT
  • INTACT_INTERACTS_WITH_GENE_PROTEIN: Removed due to obsolete source IntACT
  • INTACT_INTERACTS_WITH_PROTEIN_PROTEIN: Removed due to obsolete source IntACT
  • INTACT_NOT_INTERACTS_WITH: Removed due to obsolete source IntACT
  • METAMAP_LITE
    • new props: mesh
  • MONDO_MAP_EFO
  • MONDO_MAP_UMLS
  • MR: Renamed to MR_EVE_MR (which only consists of precomputed results from source MR EvE)
    • removed props: log10pval
  • OBS_COR
  • OPENTARGETS_DRUG_TO_DISEASE
  • OPENTARGETS_DRUG_TO_TARGET
  • PATHWAY_TO_DISEASE: Removed due to overhauled source Reactome
  • PATHWAY_TO_LITERATURE: Removed due to overhauled source Reactome
  • PRECEDING_EVENT: Removed due to overhauled source Reactome
  • PROTEIN_IN_EVENT: Removed due to overhauled source Reactome
  • PROTEIN_TO_DISEASE: Removed due to overhauled source Reactome
  • PROTEIN_TO_LITERATURE: Removed due to overhauled source Reactome
  • PROTEIN_IN_PATHWAY
  • PRS
  • SEM_GENE: Renamed to TERM_TO_GENE
  • SEM_OBJ: Renamed to SEMMEDDB_OBJ
  • SEM_PREDICATE: Renamed to SEMMEDDB_PREDICATE
  • SEM_SUB: Renamed to SEMMEDDB_SUB
  • SEM_TO_LIT: Renamed to SEMMEDDB_TO_LIT
  • STRING_INTERACT_WITH
  • TOPHITS: Renamed to OPENGWAS_TOPHITS
  • VARIANT_TO_GENE
  • XQTL_MULTI_SNP_MR
  • XQTL_SINGLE_SNP_MR_GENE_GWAS
  • XQTL_SINGLE_SNP_MR_SNP_GENE

New meta rels

  • BIORXIV_OBJ, BIORXIV_PREDICATE, BIORXIV_SUB, BIORXIV_TO_LIT
  • MEDRXIV_OBJ, MEDRXIV_PREDICATE, MEDRXIV_SUB, MEDRXIV_TO_LIT
  • GWAS_EFO_EBI
  • PATHWAY_CHILD_OF

Data sources

New data sources

  • Annotation of EBI GWAS traits to EFO
  • ClinVar

Removed data sources

  • IntAct: We removed IntAct as its import pipeline to EpiGraphDB is not being maintained at the moment. We will keep this under review.

Overhauled / updated data sources

  • Reactome
  • SemMedDB
  • MR-EvE

Graph database and cypher

  • EpiGraphDB graph database is now built on neo4j v4, as a side effect the following cypher will no longer return parsible dictionary structure to the API MATCH (n)-[r]-(m) RETURN n, r, m, instead use MATCH (n)-[r]-(m) RETURN n, properties(r) as r, m

API

Changes in the API are generally compatibility updates regarding the database.

Endpoint changes:

  • POST /cypher/builder/plain: Removed. Users can use POST /cypher to send cypher queries.

Web UI

We have added a search page to display results from the header search bar.


R package

Package version 0.2.2 now works with EpiGraphDB platform 1.0.0.