Chado for evolutionary biology
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Chado is a relational database schema for evolutionary science. It has several key modules including sequence, cv (controlled vocabularies), phenotype, and phylogeny. The cv module stores ontologies and terminologies. The phenotype module currently uses an EAV model but may need extensions. The phylogeny module allows storing and querying of evolutionary trees, though linking phenotypes to phylogenies remains a challenge. Overall, Chado provides an extensible framework but some parts like phenotype modeling require more development.
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Graphical UI Tools for Big Data Models
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Which ID (cv_id) corresponds to the GO ontology stored in the database.docx
Which ID (cv_id) corresponds to the GO ontology stored in the database? How is this related in MYSQL? Select xx FRom XX? Tables do not have cv_id or ontology so I am confused at where to combine this data to find \'GO\'
analysis |
| analysisfeature |
| analysisprop |
| cm_blast |
| cm_cluster_members |
| cm_clusters |
| cm_cvterms |
| cm_gene_structure |
| cm_genes |
| cm_proteins |
| cv |
| cvterm |
| cvterm_dbxref |
| cvterm_relationship |
| cvtermpath |
| cvtermprop |
| cvtermsynonym |
| db |
| dbxref |
| dbxrefprop |
| feature |
| feature_cvterm |
| feature_cvterm_dbxref |
| feature_cvterm_pub |
| feature_cvtermprop |
| feature_dbxref |
| feature_pub |
| feature_relationship |
| feature_relationship_pub |
| feature_relationshipprop |
| feature_relprop_pub |
| feature_synonym |
| featureloc |
| featureprop |
| featureprop_pub |
| organism |
| organism_dbxref |
| organismprop |
| project |
| pub |
| pub_dbxref |
| pub_relationship |
| pubauthor |
| pubprop |
| synonym |
| tableinfo
Solution
Answer:
GO stands for Gene Ontology which is a framework for model of biology defining classes/concepts used to describe gene function and relationship among these.
Data related to ontology can be accessed through GO database. This database is generated from most recent version of ontology and is available in various formats and channels. MySQL is one of them. Other fromats are OBO XML, OWL and RDF XML etc.
You have not specified which kind of bioinformatics schema you are using. It is important to know the type of schema because there many such format available like Chado, BioSQL. GO schema is the predecessor of all such schemas. However, there are other schemas, like Chado, that contain different types of ontologies.
CV or \"Controlled Vocabulary\" is anoother name for ontology and \'cv\' table in database represents this. It is composed of cvterms and retationships among them. In this table, name or similar column will provide the reference to an ontology.
Hence, you are advised to browsed the columns of \'cv\' to find the referenece(s) for your desired ontology. It is likely that you will get a reference inb this table.
.
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