Matthias König
and
Jan Grzegorzewski
[^] AnnotateDB
(pronounced annotated bee
) is a database with web frontend for mapping of annotations found in computational models in biology.
AnnotateDB
is accessible via https://annotatedb.com.
- Our mission is to provide mapped annotation resources which simplify annotation of computational models and mapping of entities in such models.
- Our vision is to provide a single integrated knowledge resource which simplifies mapping between commonly occurring annotations in biological models and data.
AnnotateDB
provides a high quality mapping of annotations on each other based on existing resources.
Features are
- annotation mappings from multiple sources
- support for custom annotation mappings
- support for
qualifiers
, i.e., more detailed relationships between annotations - support for evidence of annotations, i.e., provenance about the source and method with which the mapping was inferred
- direct access to the
postgres
database docker
anddocker-compose
scripts for easy local setup and deploymentREST
based web interfaceelastisearch
based indexing and search (Theelasticsearch
end points are still in development and will be part ofv0.2.0
)
AnnotateDB
is accessible under the following licenses
- Source Code: LGPLv3
- Documentation: CC BY-SA 4.0
[^] AnnotateDB
is distributed as docker
containers, requiring a working docker
and docker-compose
installation.
To install AnnotateDB
locally use
# clone or pull the latest source code
git clone https://github.com/matthiaskoenig/annotatedb.git
cd annotatedb
# set environment variables
set -a && source .env.local
# create/rebuild all docker containers
./docker-purge.sh
# restore database
./adb_restore.sh
# elasticsearch indexing
./elasticsearch.sh
This creates the following services
adb_postgres
http://localhost:5434/ - postgres databaseadb_backend
http://localhost:5434/ - django backendadb_frontend
http://localhost:8090/ - vue.js frontendadb_elasticsearch
http://localhost:9124/ - elasticsearch instance
In later releases the installation will be simplified, i.e., prebuild docker containers will be available from dockerhub (see #32).
[^] AnnotateDB
provides REST
endpoints for querying the database at https://annotatedb.com/api/v1.
Some examples
- to query the
collections
use:https://annotatedb.com/api/v1/collections/?format=json
. - to query the
mappings
use:https://annotatedb.com/api/v1/mappings/?format=json
. - to query a single
collection
usehttps://annotatedb.com/api/v1/collections/sbo/?format=json
.
This will return the information on the collection
, in this example for sbo
{
"namespace":"sbo",
"miriam":true,
"name":"Systems Biology Ontology",
"idpattern":"^SBO:\\d{7}$",
"urlpattern":"https://identifiers.org/sbo/{$id}"
}
Currently only basic REST
endpoints are available. With the introduction of the elasticsearch
endpoints in v0.3.0
the REST based search will largely improve.
For now users should directly interact with the postgres database to interact
with the mappings (see information below).
[^] The postgres database is accessible via
HOST: localhost
PORT: 5434
DB: adb
USER: adb
PASSWORD: adb
The database contains the following main tables (see schema below):
adb_collection
: A data source or miriam collection for annotation or xref informationadb_annotation
: The combination of a term from a collection and the given collectionadb_mapping
: Mapping between annotations, from source annotation to target annotation. The kind of mapping is defined by the qualifier. E.g. the qualifierBQM_IS
encodes that the source annotationis
the target annotation.adb_evidence
: Evidence for the given mapping between annotations.
In addition the materialized view mapping_view
is provided which allows easy filtering and search of
mapped annotations and annotation synonyms. For most use cases the mapping_view
is the table to work with.
For instance query the bigg.metabolite
for a given chebi
identifier via
SELECT source_term FROM mapping_view
WHERE (target_term = 'CHEBI:698' AND
target_namespace = 'chebi' AND
source_namespace = 'bigg.metabolite' AND
qualifier = 'IS');
which results in
('10fthf',)
A more comprehensive list of SQL queries and use cases is provided here with output here.
[^] AnnotateDB
uses the following data sources:
Information on collections is based mainly on identifiers.org.
Collections were parsed with sbmlutils
.
A major source of annotation mappings is the BiGG Database
with information used from the latest database release. AnnotateDB
currently includes BiGG-v1.5
.
[^] This section provides an overview of major changes and releases
- security fixes
- django update (>3.0), elasticsearch update (7.7.1), postgres update (12.3),
- replacing deprecated
django-rest-swagger
withdrf-yasg
- bug fixes admin interface
- bug fixes frontend server
- enforcing uniqueness of mappings & removing duplicates
- materialized views
- detailed postgres examples
- updated documentation
- vue frontend
- bigg mappings import
- database release files
- django development server
- first database schema
- docker-compose files for backend, database and elasticsearch
[^] We acknowledge
- Dr. Andreas Dräger
- Thomas Zajac
for their input and discussions.
© 2019-2020 Matthias König & Jan Grzegorzewski