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.
Steps to follow:
- Generate globi tsv file
cd modGLoBI
python globiDown.py <Globi tsv-file> categories.txt qlever/data/<output-file>
- Generate ontology mappings [LifestageNames (DevelopmentalStage) and BodyPartNames (AnatomicalEntity)]
cd ontology
python matchNamesToOntology.py <input-file> <output-file>
e.g:
python matchNamesToOntology.py data/globi/unmappedBodyPartNamesGlobi.csv data/globi/mappedBodyPartNamesGlobi.csv
- Generate triples
Place the tsv-files in qlever/data.
a) Make a config file config.txt (present in this folder) and update files and then run the respective scripts
cd src
python makeTriples_trydb_rdf_v1.py
python makeTriples_globi_rdf_v1.py
python makeTriples_taxonomy_rdf_v1.py
OR
b) If config file is not present, then add command-line arguments
cd src
python makeTriples_trydb_rdf_v1.py <trydb tsv-file> <enpkg wd ids> <output-file>
python makeTriples_globi_rdf_v1.py <globi tsv-file> <enpkg wd ids> <output-file>
python makeTriples_taxonomy_rdf_v1.py <taxonomy tsv-file> <enpkg wd ids> <output-file>
- Generate qlever sparql endpoint
a) Generate first set of index and start the server
cd qlever
qlever --qleverfile Qlever.try_globi index --overwrite-existing --parallel-parsing false
qlever --qleverfile Qlever.try_globi start
b) Generate void file for the triples
Obtain void-generator jar file
java -jar void-generator-0.6-SNAPSHOT-uber.jar -r "http://localhost:<port-name>" --void-file void-trydbglobi1.ttl -i http://localhost:<port-name>/.voidX/ --max-concurrency 1 -f
c) Generate second set of index and start the server for querying
qlever --qleverfile Qlever.try_globi stop
qlever --qleverfile Qlever.try_globi.spql_editor index --overwrite-existing --parallel-parsing false```
qlever --qleverfile Qlever.try_globi start
- Obtain the html file from sparql-editor
a) Copy the index.html file obtained to qlever/sparql-editor-index.html. Add the appropriate js-file and the sparql endpoint to the html file.
b) Start the server inside the qlever directory
python cors_server.py
c) Open the qlever/sparql-editor-index.html to query and explore the class overview.
Tree structure and comments for each file
.
├── modGLoBI #folder for automating globi tsv file
│ ├── categories.txt #taxonomy to be considered for globi
│ └── globiDwn.py #script to generate tsv file
├── ontology
│ ├── data
│ │ ├── globi #folder for ontology matches of body part and life stage names to ontologies like UBERON, PO, ENVO, PATO, etc.
│ │ │ ├── correctedBodyPartNamesGlobi.csv
│ │ │ ├── mappedBodyPartNamesGlobi.csv
│ │ │ ├── unmappedBodyPartNamesGlobi.csv
│ │ │ ├── correctedLifeStageNamesGlobi.csv
│ │ │ ├── mappedLifeStageNamesGlobi.csv
│ │ │ │── unmappedLifeStageNamesGlobi.csv
│ │ │ │── correctedBiologicalSexNames.tsv
│ │ │ ├── mappedBiologicalSexNames.tsv
│ │ │ ├── unmappedBiologicalSexNames.tsv
│ │ ├── README.md
│ │ └── trydb #folder for ontology matches of units from trydb to quft
│ │ ├── EmiMappingToTryDb.txt #mapping of units (not in qudt)
│ │ └── qudtMappingToTryDb.txt #mapping of units present in qudt
│ └── matchNamesToOntology.py #given a list of names, match them to ontology entities from UBERON, PO, ENVO, PATO, etc.
│── src #main codes and functions for generating triples in turtle format
│ ├── config.txt #config file with locations to input, accessory and output files
│ ├── functions
│ │ │── data_processing.py #functions to parse files, dataframes and strings
│ │ └── matchNamesBiologicalGender.py #function to assign biological gender while maing the rdf triples
│ ├── 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
├── qlever #settings for qlever
│ ├── cors_server.py #start a server with CORS enabled in python
│ ├── data #data for building qlever index
│ │ └── accessory #folder with accessory files
│ ├── Qlever.try_globi #configuration for qlever without void and example ttls
│ ├── Qlever.try_globi.spql_editor #configuration for qlever with -void, examples- required for sparql-editor
│ └── sparql_editor_index.html #implement sparql editor
├── README.md
└── requirements.txt #pip install -r requirements.txt