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
: We have dropped the use of a Meta node for metadata information.Meta
Disease
Drug
Efo
Event
: Removed due to overhaul of sourceReactome
Gene
- new props:
biomart_source
- new props:
Gwas
- new props:
build
- new props:
Literature
- new props:
doi
- renamed props:
pubmid_id
:id
- new props:
Pathway
- removed props:
in_disease
- renamed props:
reactome_id
:id
- removed props:
Protein
- new props:
name
- new props:
SemmedTriple
: Renamed toLiteratureTriple
. Entity labels are now removed fromLiteratureTriple
s and only CUI id remain. Users will need to match fromLiteratureTerm
to get the entity labels.- removed props:
count
,subject_name
,object_name
,subject_type
,object_type
- new props:
name
(mergesubject_name
,predicate
,object_name
together)
- removed props:
SemmedTerm
: Renamed toLiteratureTerm
- removed props:
count
- removed props:
Tissue
- renamed props:
tissue
:{id, name}
- renamed props:
Variant
- new props:
pos
,chr
,ref
,alt
,build
- new props:
Meta rels
BN_GEN_COR
: Renamed toGEN_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
- renamed props:
CPIC
EFO_CHILD_OF
EVENT_IN_PATHWAY
: Removed due to overhauled sourceReactome
EXPRESSED_IN
GENE_TO_LITERATURE
: Removed due to overhauled sourceReactome
GENE_TO_PROTEIN
GWAS_NLP
GWAS_NLP_EFO
GWAS_SEM
: Renamed toGWAS_TO_LITERATURE_TRIPLE
GWAS_TO_LIT
: Renamed toGWAS_TO_LITERATURE
GWAS_TO_VARIANT
INTACT_INTERACTS_WITH_GENE_GENE
: Removed due to obsolete sourceIntACT
INTACT_INTERACTS_WITH_GENE_PROTEIN
: Removed due to obsolete sourceIntACT
INTACT_INTERACTS_WITH_PROTEIN_PROTEIN
: Removed due to obsolete sourceIntACT
INTACT_NOT_INTERACTS_WITH
: Removed due to obsolete sourceIntACT
METAMAP_LITE
- new props:
mesh
- new props:
MONDO_MAP_EFO
MONDO_MAP_UMLS
MR
: Renamed toMR_EVE_MR
(which only consists of precomputed results from sourceMR EvE
)- removed props:
log10pval
- removed props:
OBS_COR
OPENTARGETS_DRUG_TO_DISEASE
OPENTARGETS_DRUG_TO_TARGET
PATHWAY_TO_DISEASE
: Removed due to overhauled sourceReactome
PATHWAY_TO_LITERATURE
: Removed due to overhauled sourceReactome
PRECEDING_EVENT
: Removed due to overhauled sourceReactome
PROTEIN_IN_EVENT
: Removed due to overhauled sourceReactome
PROTEIN_TO_DISEASE
: Removed due to overhauled sourceReactome
PROTEIN_TO_LITERATURE
: Removed due to overhauled sourceReactome
PROTEIN_IN_PATHWAY
PRS
SEM_GENE
: Renamed toTERM_TO_GENE
SEM_OBJ
: Renamed toSEMMEDDB_OBJ
SEM_PREDICATE
: Renamed toSEMMEDDB_PREDICATE
SEM_SUB
: Renamed toSEMMEDDB_SUB
SEM_TO_LIT
: Renamed toSEMMEDDB_TO_LIT
STRING_INTERACT_WITH
TOPHITS
: Renamed toOPENGWAS_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 useMATCH (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 usePOST /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.