To-Do List
To-Do List#
The following problems are known issues which will be solved, but are yet to be adressed:
Todo
When fixing queries, fix the main subscript also
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.annotate_using_wikidata, line 8.)
Todo
CAMBIAR NOMBRE A LOS MESH PARA INDICAR EL TIPO. AÑADIR NAME A LOS WIKIDATA
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 6.)
Todo
FIX THE REPEAT TRANSACTION FUNCTION
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 7.)
Todo
Match partial InChI based on DICE-MACCS
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 8.)
Todo
QUE FUNCIONE -> ACTUALMENTE ESTA SECCION RALENTIZA MAZO
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 9.)
Todo
CHECK APOC IS INSTALLED
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 10.)
Todo
FIX MAIN
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 11.)
Todo
MERGE BY INCHI, METANETX ID
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 12.)
Todo
Fix find_protein_interactions_in_metanetx
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 13.)
Todo
Mover esa funcion de setup a misc
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 14.)
Todo
EDIT conf.py
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 15.)
Todo
Document the following Schema Changes: * For Subject, we have a composite PK: Exposome_Explorer_ID, Age, Gender e Information * Now, more diseases will have a WikiData_ID and a related MeSH. This will help with networking. And, this diseases dont even need to be a part of a cancer! * The Gene nodes no longer exist in the full db? -> They do
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/main.py:docstring of CanGraph.main.main, line 17.)
Todo
Make it download the image
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/miscelaneous.py:docstring of CanGraph.miscelaneous.call_db_schema_visualization, line 7.)
Todo
In some other parts of the script, sequences are being added as properties on Protein nodes. A common format should be set.
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifyDrugBank/build_database.py:docstring of CanGraph.GraphifyDrugBank.build_database.add_sequences, line 12.)
Todo
Investigate https://stackoverflow.com/questions/14026217/using-neo4j-distinct-and-order-by-on-different-properties
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifyDrugBank/build_database.py:docstring of CanGraph.GraphifyDrugBank.build_database.add_targets_enzymes_carriers_and_transporters, line 26.)
Todo
It would be nice to be able to distinguish between experimental and predicted properties
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifyHMDB/build_database.py:docstring of CanGraph.GraphifyHMDB.build_database.add_biological_properties, line 16.)
Todo
It would be nice to be able to distinguish between experimental and predicted properties
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifyHMDB/build_database.py:docstring of CanGraph.GraphifyHMDB.build_database.add_experimental_properties, line 16.)
Todo
It would be nice to be able to distinguish between experimental and predicted properties
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifyHMDB/build_database.py:docstring of CanGraph.GraphifyHMDB.build_database.add_predicted_properties, line 16.)
Todo
This file is really big. It could be divided into smaller ones.
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifySMPDB/build_database.py:docstring of CanGraph.GraphifySMPDB.build_database.add_pathways, line 12.)
Todo
Why is the SMPDB_ID property called like that and not SMDB_ID?
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/GraphifySMPDB/build_database.py:docstring of CanGraph.GraphifySMPDB.build_database.add_proteins, line 15.)
Todo
Might include P684 “Orthologues” for more info (it crashed java)
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/QueryWikidata/build_database.py:docstring of CanGraph.QueryWikidata.build_database.add_gene_info, line 13.)
Todo
Might include P527 “has part or parts” for more info (it crashed java)
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/QueryWikidata/build_database.py:docstring of CanGraph.QueryWikidata.build_database.add_metabolite_info, line 17.)
Todo
ADD ROLE to metabolite interactions
(The original entry is located in /home/pablo/Documentos/Trabajos del cole/UNI/IARC/Work/CanGraph/QueryWikidata/build_database.py:docstring of CanGraph.QueryWikidata.build_database.add_more_drug_info, line 13.)