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Mondo content statistics

Mondo Statistics

The Mondo statistics include:

  • disease classes
  • terms with definitions
  • xrefs
  • exact, related, narrow, and broad synonyms
  • rare diseases
  • cancer diseases
  • infectious diseases
  • hereditary diseases

When creating the stats, a set of SPARQL queries are run on the reasoned version of Mondo. This reasoned version of Mondo is created from the most recent version of mondo-edit.obo in your current GitHub branch.

Create Mondo Stats

Create Mondo stats from the mondo/src/ontology directory as:
sh run.sh make create-mondo-stats

The result file is created in mondo/src/ontology/reports/mondo_stats. This file is ignored by git so you will not see it highlighted as a changed file.

SPARQL Queries

All queries used to create the Mondo statistics are in the src/sparql/mondo_stats/ directory.

Disease terms

  • Definition = all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE, i.e. the IRI starts with http://purl.obolibrary.org/obo/MONDO_
  • SPARQL query - see COUNT-classes.sparql

Term definitions

  • Definition = all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease that have a MONDO CURIE and have a definition
  • SPARQL query - see COUNT-classes-with-definitions.sparql

Database cross references

  • Definition = count of all xrefs that are found on all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE
  • SPARQL query - COUNT-xrefs.sparql

Exact Synonyms

  • Definition = count of all exact synonyms that are found on all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE
  • SPARQL query - see COUNT-exact-synonyms.sparql
  • Definition = count of all related synonyms that are found on all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE
  • SPARQL query - see COUNT-related-synonyms.sparql

Narrow Synonyms

  • Definition = count of all narrow synonyms that are found on all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE
  • SPARQL query - see COUNT-narrow-synonyms.sparql

Broad Synonyms

  • Definition = count of all broad synonyms that are found on all unique non-obsolete classes (asserted and inferred) that are children of MONDO:0000001 disease and have a MONDO CURIE
  • SPARQL query - see COUNT-broad-synonyms.sparql

Rare Diseases

  • Definition = all unique non-obsolete classes (asserted or inferred) that are children of MONDO:0000001 disease and are in the "rare" subset
  • SPARQL query - see COUNT-rare-diseases-classes.sparql

Infectious Diseases

  • Definition = all unique non-obsolete classes (asserted or inferred) that are children of of MONDO:0005550 'infectious disease' and have a Mondo CURIE
  • SPARQL query - see COUNT-infectious-diseases.sparql

Cancer Diseases

  • Definition = all unique non-obsolete classes (asserted or inferred) that are children of of MONDO:0045024 'cancer or benign tumor' and have a Mondo CURIE
  • SPARQL query - see COUNT-cancer-diseases.sparql

Mendelian Diseases

  • Definition = all unique non-obsolete classes (asserted or inferred) that are children of MONDO:0003847 'hereditary disease' and have a Mondo CURIE
  • SPARQL query - see COUNT-hereditary-disease.sparql

Query Execution

This section includes examples of how to run an individual statistics query and how all queries can be run together as specified in the create-mondo-stats make goal.

Run Individual Query

  • Any query can be run individually with the general pattern of: robot query -i reasoned.owl -q ../sparql/mondo_stats/<MY-QUERY-OF-INTEREST.sparql> <RESULTS.csv>

  • Working example: 

$ robot query -i reasoned.owl -q ../sparql/mondo_stats/COUNT-disease-classes.sparql ../sparql/reports/mondo_stats/diseaseClass_count.tsv

Run multiple ROBOT queries in one command

robot query --input reasoned.owl \
--query ../sparql/mondo_stats/COUNT-classes.sparql ../sparql/reports/mondo_stats/tmp_01_class_count.tsv \
--query ../sparql/mondo_stats/COUNT-classes-with-definitions.sparql ../sparql/reports/mondo_stats/tmp_03_classDefinition_count.tsv \
--query ../sparql/mondo_stats/COUNT-xrefs.sparql ../sparql/reports/mondo_stats/tmp_02_xref_count.tsv \
--query ../sparql/mondo_stats/COUNT-exact-synonyms.sparql ../sparql/reports/mondo_stats/tmp_04_exactSynonym_count.tsv \
--query ../sparql/mondo_stats/COUNT-related-synonyms.sparql ../sparql/reports/mondo_stats/tmp_05_relatedSynonym_count.tsv \
--query ../sparql/mondo_stats/COUNT-narrow-synonyms.sparql ../sparql/reports/mondo_stats/tmp_06_narrowSynonym_count.tsv \
--query ../sparql/mondo_stats/COUNT-broad-synonyms.sparql ../sparql/reports/mondo_stats/tmp_07_broadSynonym_count.tsv \
--query ../sparql/mondo_stats/COUNT-rare-diseases-classes.sparql  ../sparql/reports/mondo_stats/tmp_08_rareDiseaseClass_count.tsv \
--query ../sparql/mondo_stats/COUNT-infectious-diseases.sparql ../sparql/reports/mondo_stats/tmp_09_infectiousDiseaseClass_count.tsv \
--query ../sparql/mondo_stats/COUNT-cancer-diseases.sparql ../sparql/reports/mondo_stats/tmp_10_cancerDiseaseClass_count.tsv \
--query ../sparql/mondo_stats/COUNT-hereditary-diseases.sparql ../sparql/reports/mondo_stats/tmp_11_hereditaryDiseaseClass_count.tsv

NOTE: A number was included in the result file name so the combined file will have the contents in the desired order of information.

  • Combine all "tmp_" result files into 1 file
echo "All Combined Results created on: $(date)" > ../sparql/reports/mondo_stats/all_mondo_stats.txt
cat ../sparql/reports/mondo_stats/tmp_* >> ../sparql/reports/mondo_stats/all_mondo_stats.txt
  • Remove all "tmp_" result files
rm ../sparql/reports/mondo_stats/tmp_*