Cellosaurus API

From the CALIPHO group of the SIB - Swiss Institute of Bioinformatics

Provides a programmatic access to the Cellosaurus, a knowledge resource on cell lines

Cellosaurus API : https://api.cellosaurus.org/

See also cellosaurus website : https://www.cellosaurus.org/

Prerequisites to local installation

• Linux or Mac platofrm
• git installed
• curl or equivalent installed
• python 3.9 installed, see cellapi_builder.py and main.py for modules to be installed
• solr 8.11.1 or later installed

Install latest cellosaurus-api code

code_source="https://github.com/calipho-sib/cellosaurus-api.git" 
git checkout $code_source
cd cellosaurus-api

Setup of solr collection for cellosaurus-api (only on first installation)

• Create a symbolic link 'solr' in the api directory pointing to your to your solr install directory

ln -s /your/solr8.11.1-or-later/home/directory/ solr

• Start solr service, create cellosaurus solr collection 'pamcore1'

./solr_service.sh start
./solr/bin/solr create -c pamcore1

• Link cellosaurus-api solr config to 'pamcore1' collection

cd solr/server/solr/poumcore1/conf
mv managed-schema managed-schema.ori 
mv solrconfig.xml solrconfig.xml.ori
ln -s ../../../../../solr_config/schema.xml
ln -s ../../../../../solr_config/solrconfig.xml

• Back to cellosaurus-api base directory and restart service to take into account new schema of 'pamcore1' collection

cd ../../../../../
./solr_service.sh restart

Retrieve latest cellosaurus data

data_source="https://ftp.expasy.org/databases/cellosaurus"
mkdir -p data_in
cd data_in
curl "$code_source/cellosaurus.txt" > cellosaurus.txt
curl "$code_source/cellosaurus_refs.txt" > cellosaurus_refs.txt
curl "$code_source/cellosaurus.xml" > cellosaurus.xml

Build api indexes and solr data

• Go back to cellosaurus-api base directory

cd .. 

• Build api index files in serial directory

mkdir -p serial
python3.9 cellapi_builder.py BUILD

• Build solr input files in solr_data directory (long process, few minutes)

mkdir -p solr_data
python3.9 cellapi_builder.py SOLR

• Reload solr data in solr 'pamcore1' collection

./solr_service.sh restart
./solr/bin/post -c pamcore1 -d "<delete><query>*:*</query></delete>"
./solr/bin/post -c pamcore1 solr_data/data*.xml

How to build RDF data

python3.9 cellapi_builder.py RDF
python3.9 cellapi_builder.py LOAD_RDF data
python3.9 cellapi_builder.py ONTO
python3.9 cellapi_builder.py LOAD_RDF onto

How to restart services

./api_service.sh stop
./api_service.sh start
./solr_service.sh stop
./solr_service.sh start

How to connect to services

Use your browser and go to

• http://localhost:8088/
• http://localhost:8983/solr

Reference

Bairoch A. The Cellosaurus, a cell line knowledge resource. J. Biomol. Tech. 29:25-38(2018). DOI: 10.7171/jbt.18-2902-002; PMID: 29805321 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945021/

Powered by

• git : https://git-scm.com/
• github : https://github.com/
• python : https://www.python.org/
• fastAPI : https://fastapi.tiangolo.com/
• solr : https://solr.apache.org/

Licensing

This work is licensed under a GNU General Public License version 3.