Computing basic metrics for the EDAM ontology.
java -jar target/EDAMetrics-0.0.1-SNAPSHOT-standalone.jar -i ~/Desktop/EDAM_1.18.owl -h
usage: EDAM-Metrics [-cbs] [-cd] [-ces] [-cf] [-cns] [-co] [-ct] [-dd]
[-df] [-do] [-dt] [-h] [-i <input_owl_file>] [-s] [-sbs] [-ses]
[-sns] [-v]
EDAM-Metrics aims at computing basic metrics on the EDAM ontology
-cbs,--count_broad_synonyms count broad synonyms
-cd,--count_data count data
-ces,--count_exact_synonyms count exact synonyms
-cf,--count_formats count formats
-cns,--count_narrow_synonyms count narrow synonyms
-co,--count_operations count operations
-ct,--count_topics count topics
-dd,--list_deep_data list deep data (6+ nested levels)
-df,--list_deep_formats list deep formats (6+ nested
levels)
-do,--list_deep_operations list deep operations (6+ nested
levels)
-dt,--list_deep_topics list deep topics (6+ nested
levels)
-h,--help print the help
-i,--input_owl_file <input_owl_file> The input ontology in OWL
-s,--summary outputs a summay table
-sbs,--sort_broad_synonyms sort broad synonyms
-ses,--sort_exact_synonyms sort exact synonyms
-sns,--sort_narrow_synonyms sort narrow synonyms
-v,--version print the version information and
exit
java -jar target/EDAMetrics-0.0.1-SNAPSHOT-standalone.jar -i ~/Desktop/EDAM_1.18.owl --summary
EdamVitalMetrics{exactSynonyms=1109, narrowSynonyms=705, broadSynonyms=60, data=954, topics=238, formats=499, operations=528}
java -jar target/EDAMetrics-0.0.1-SNAPSHOT-standalone.jar -i ~/Desktop/EDAM_1.18.owl -do
-----------------------------------------------------------------------------------------------------------
| edam_deep_op | label |
===========================================================================================================
| <http://edamontology.org/operation_0441> | "Transcription regulatory element prediction (DNA-cis)" |
| <http://edamontology.org/operation_0242> | "Conserved transcription regulatory sequence identification" |
| <http://edamontology.org/operation_0391> | "Protein distance matrix calculation" |
| <http://edamontology.org/operation_0544> | "Phylogenetic species tree construction" |
| <http://edamontology.org/operation_0434> | "Integrated gene prediction" |
| <http://edamontology.org/operation_3225> | "Variant classification" |
| <http://edamontology.org/operation_3217> | "Scaffold gap completion" |
| <http://edamontology.org/operation_0393> | "Residue cluster calculation" |
| <http://edamontology.org/operation_0445> | "Transcription factor binding site prediction" |
| <http://edamontology.org/operation_0464> | "tRNA gene prediction" |
| <http://edamontology.org/operation_0472> | "GPCR prediction" |
| <http://edamontology.org/operation_3202> | "Polymorphism detection" |
| <http://edamontology.org/operation_3663> | "Homology-based gene prediction" |
| <http://edamontology.org/operation_0440> | "Promoter prediction" |
| <http://edamontology.org/operation_0481> | "Protein modelling (loops)" |
| <http://edamontology.org/operation_0479> | "Protein modelling (backbone)" |
etc.
java -jar target/EDAMetrics-0.0.1-SNAPSHOT-standalone.jar -i ~/Desktop/EDAM_1.18.owl -sns
-----------------------------------------------------------------------------------------------------------------------------
| edam_class | label | narrow_syn_count |
=============================================================================================================================
| <http://edamontology.org/topic_0749> | "Transcription factors and regulatory sites" | 17 |
| <http://edamontology.org/topic_0602> | "Molecular interactions, pathways and networks" | 15 |
| <http://edamontology.org/data_2603> | "Gene expression data" | 14 |
| <http://edamontology.org/topic_0659> | "Functional, regulatory and non-coding RNA" | 14 |
| <http://edamontology.org/topic_0154> | "Small molecules" | 13 |
| <http://edamontology.org/topic_3168> | "Sequencing" | 12 |
| <http://edamontology.org/topic_3512> | "Gene transcripts" | 12 |
| <http://edamontology.org/topic_3518> | "Microarray experiment" | 12 |
| <http://edamontology.org/operation_0004> | "Operation" | 8 |
| <http://edamontology.org/topic_0157> | "Sequence composition, complexity and repeats" | 8 |
| <http://edamontology.org/topic_0736> | "Protein folds and structural domains" | 8 |
| <http://edamontology.org/topic_3674> | "Methylated DNA immunoprecipitation" | 8 |
| <http://edamontology.org/topic_0082> | "Structure prediction" | 7 |
| <http://edamontology.org/topic_2885> | "DNA polymorphism" | 7 |
| <http://edamontology.org/topic_3375> | "Drug metabolism" | 7 |
| <http://edamontology.org/topic_3489> | "Database management" | 7 |
| <http://edamontology.org/data_1355> | "Protein signature" | 6 |
| <http://edamontology.org/data_3724> | "Cultivation parameter" | 6 |
| <http://edamontology.org/operation_0239> | "Sequence motif recognition" | 6 |
| <http://edamontology.org/operation_0308> | "PCR primer design" | 6 |
| <http://edamontology.org/operation_2950> | "Residue distance calculation" | 6 |
| <http://edamontology.org/operation_3092> | "Protein feature detection" | 6 |
| <http://edamontology.org/operation_3280> | "Named-entity and concept recognition" | 6 |
| <http://edamontology.org/topic_0097> | "Nucleic acid structure analysis" | 6 |
| <http://edamontology.org/topic_0128> | "Protein interactions" | 6 |
| <http://edamontology.org/topic_0160> | "Sequence sites, features and motifs" | 6 |
| <http://edamontology.org/topic_0593> | "NMR" | 6 |
| <http://edamontology.org/topic_0611> | "Electron microscopy" | 6 |
| <http://edamontology.org/topic_3070> | "Biology" | 6 |
| <http://edamontology.org/topic_3125> | "DNA binding sites" | 6 |
| <http://edamontology.org/operation_0314> | "Gene expression profiling" | 5 |
| <http://edamontology.org/operation_0415> | "Nucleic acid feature detection" | 5 |
| <http://edamontology.org/operation_3227> | "Variant calling" | 5 |
| <http://edamontology.org/topic_0084> | "Phylogeny" | 5 |
etc.