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Biomarker Database (rewrite and utilities)

License: Apache License 2.0

Python 97.02% Shell 0.79% Dockerfile 2.19%

cancer-detection biomarker

edrn.bmdb's Introduction

edrn.bmdb

This package provides the Early Detection Research Network's Biomarker Database (BMDB) or its utilities.

Features

Standalone RDF generation from a BMDB database.
And RDF server serving RDF over HTTP.
Various reports requested by @mryan4.

Examples

You don't want to see any examples of this.

Documentation

Partial documentation for end users can be found in the "docs" folder (probably a blatant lie).

Translations

This product has not been translated into any other languages than US English.

Installation

Try pip or use Docker.

Docker

Now handled by the imaging workflow of GitHub Actions.

Handy Focus BMDB Tables in MySQL

acl
auditor
biomarker_datasets
biomarker_names
biomarker_resources
biomarker_study_data
biomarker_study_data_publications
biomarker_study_data_resources
biomarker_study_data_sensitivities
biomarkers
biomarkers_publications
biomarkers_search
organ_data
organ_data_publications
organ_data_resources
organ_data_terms
organs
paneldata
people
person_study
pis
publications
publications_studies
publications_study_data
search_aliases
search_biomarker_names
search_names_organs
search_organs
search_primary_names
search_view
sensitivities
sensitivities_study_data
sites
sites_studies
studies
study_data
study_data_resources
study_resources
terms
users

Contribute

Issue Tracker: https://github.com/EDRN/edrn.bmdb/issues
Source Code: https://github.com/EDRN/edrn.bmdb

Support

If you are having issues, please let us know. We have a mailing list located at: [email protected]

License

The project is licensed under the ALv2.

edrn.bmdb's People

Contributors

Watchers

edrn.bmdb's Issues

RDF server loses database connection

After a while, queries into the RDF service for the Focus Bio Marker Data Base (BMDB) fail and emit this in the logs:

focusbmdb-rdf    |   File "/app/src/edrn/bmdb/server.py", line 50, in __call__
focusbmdb-rdf    |     cursor.execute('SELECT COUNT(*) FROM `biomarkers`')
focusbmdb-rdf    |   File "/app/eggs/PyMySQL-0.10.0-py3.8.egg/pymysql/cursors.py", line 163, in execute
focusbmdb-rdf    |     result = self._query(query)
focusbmdb-rdf    |   File "/app/eggs/PyMySQL-0.10.0-py3.8.egg/pymysql/cursors.py", line 321, in _query
focusbmdb-rdf    |     conn.query(q)
focusbmdb-rdf    |   File "/app/eggs/PyMySQL-0.10.0-py3.8.egg/pymysql/connections.py", line 504, in query
focusbmdb-rdf    |     self._execute_command(COMMAND.COM_QUERY, sql)
focusbmdb-rdf    |   File "/app/eggs/PyMySQL-0.10.0-py3.8.egg/pymysql/connections.py", line 742, in _execute_command
focusbmdb-rdf    |     raise err.InterfaceError(0, '')
focusbmdb-rdf    | pymysql.err.InterfaceError: (0, '')

This discussion suggests that having a universal connection object is the culprit. We need to create one per thread.

RDF generation needs phase at organ→study level

The EDRN Portal needs to provide biomarker phase information at the organ→study level. To do so, it must get this information from the BMDB RDF.

See: EDRN/P5#140

Python 2 → 3

This package is still using Python 2.7, which reached end of life on 2020-01-01.

Python 3 has been out 12 years. It's time to leave Python 2 behind.

Barrett's Esophagus subject URI is incorrect

BMDB RDF says that for biomarker http://edrn.jpl.nasa.gov/bmdb/biomarkers/view/53 the AssociatedDataset predicate is https://edrn-labcas.jpl.nasa.gov/labcas-ui/c/index.html?collection_id=Barretts_Esophagus_Methylation_Profile_Dataset.

However, the actual subject URI is https://edrn-labcas.jpl.nasa.gov/labcas-ui/c/index.html?collection_id=Barrett's_Esophagus_Methylation_Profile_Dataset.

There should be a "referencesStudy" predicate

The RDF generation for organ-specific information for a biomarker doesn't include the study.

The FHCRC_ID column of the study data should be used to make a <bmdb:referencesStudy> predicate whose rdf:resource is http://edrn.nci.nih.gov/data/protocols/{PROTOCOL-ID}.

Change phase literal values

Currently phases are of the form

http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Phase = One

http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Phase = Three

which is dumb for sorting purposes. But this is how ahart did it back in the day. We need to use actual numbers so we can sort properly, i.e.:

http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Phase = 1

http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Phase = 3