Creates and configures all Tripal Content Types used by KnowPulse.
- Sequence Ontology (SO): Used for chado.feature types (gene, sequence_variant, genetic_marker, chromosome, QTL, etc.) and variant types (SNP, MNP, Indel)
- Plant Ontology (PO; v2017-02-02): Used to annotate phenotypes.
- Plant Trait Ontology (TO; v2017-02-02): Used to annotate phenotypes.
- Lentil (CO_339; v2016-02-15), Chickpea (CO_338; v2016-02-15), Common Bean (CO_335; v2015-05-13) Crop Ontology: to annotate phenotypes.
- Crop Germplasm Ontology (CO_010; v2011-10-03): Used for stock.types (accession, cultivar, inbred line)
| Vocabulary | Term | Accession |
|---|---|---|
| Semantic Science | Study | SIO:001066 |
| Semantic Science | Experiment | SIO:000994 |
| EDAM | Genetic map | data:1278 |
- chado.organism table (full table)
- Organism (obi:organism)
- chado.project table (seperated using projectprop)
- Research Project (semantic science ontology; study; SIO:001066)
- Research Experiment (semantic science ontology; experiment; SIO:000994)
- Genome Assembly (Sequence Ontology; genome)
- chado.publication (full table)
- Publication (TPUB; Publication)
- chado.feature table (seperated using feature.type_id)
- Chromosome (Sequence Ontology; pseudomolecule)
- Contig (Sequence Ontology; contig)
- Variant (Sequence Ontology; sequence_variant)
- Genetic Marker (Sequence Ontology; genetic_marker)
- QTL (Sequence Ontology; QTL)
- chado.stock (seperated using stock.type_id)
- Germplasm Accession (Crop ontology; accession; CO_010:0000044)
- Breeding Cross (Crop ontology; generated germplasm(CO_010:0000255)?; breeder's line(CO_010:0000093)?, breeding material(CO_010:0000159)?)
- Registered Varieties (Sequence Ontology; cultivar; CO_010:0000029)
- Recombinant Imbred Line (Crop Ontology; inbred line; CO_010:0000162)
- chado.cvterm (specific cv_id)
- Phenotypic Trait (Trait Ontology; plant trait)
- chado.featuremap (full table)
- Genetic Map (data onotology; Map)