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: 1. Generate globi tsv file

cd modGLoBI python globiDown.py <Globi tsv-file> categories.txt qlever/data/<output-file>

1. 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

1. 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>

1. 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 ```

1. 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