This repo consists of codes for generating triples from trydb, globi and taxonomy files for the DBGI work. It also containes codes that I use often for matching random terms to ontology entities.
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├── ontology
│ ├── data
│ │ ├── globi #folder for ontology matches of body part and life stage names to ontologies like UBERON, PO, ENVO, PATO, etc.
│ │ │ ├── correctedBodyPartNamesGlobi.csv
│ │ │ ├── correctedLifeStageNamesGlobi.csv
│ │ │ ├── mappedBodyPartNamesGlobi.csv
│ │ │ ├── mappedLifeStageNamesGlobi.csv
│ │ │ ├── unmappedBodyPartNamesGlobi.csv
│ │ │ └── unmappedLifeStageNamesGlobi.csv
│ │ ├── README.md
│ │ └── trydb #folder for ontology matches of units from trydb to quft
│ │ ├── qudtMappingToTryDb_full.txt
│ │ └── qudtMappingToTryDb.txt
│ └── matchNamesToOntology.py #given a list of names, match them to ontology entities from UBERON, PO, ENVO, PATO, etc.
├── README.md
├── requirements.txt #pip install -r requirements.txt
└── src #main codes and functions for generating triples in turtle format
├── functions
│ └── data_processing.py #functions to parse files, dataframes and strings
├── makeTriples_globi_rdf_v1.py #main code to generate triples for globi interaction data
├── makeTriples_taxonomy_rdf_v1.py #main code to generate triples for taxonomy
├── makeTriples_trydb_rdf_v1.py #main code to generate triples for trydb traits data
└── turtle_custom
└── serializer.py
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├── README.md
├── requirements.txt #pip install -r requirements.txt
├── src #main codes and functions for generating triples in turtle format.
│ ├── functions
│ │ └── data_processing.py #functions to parse files, dataframes and strings
│ ├── makeTriples_taxonomy_rdf_v1.py #main code to generate triples for taxonomy
│ └── makeTriples_trydb_rdf_v1.py #main code to generate triples for trydb
├── ontology
└── matchNamesToOntology.py #given a list of names, match them to ontology entities from UBERON, PO, or ENVO