with from

	CACAO the intercollegiate annotation competition!

The Community Assessment of Community Annotation with Ontologies (CACAO) is a competition for teams of undergrads around the world to improve the functional annotation of genes. CACAO was developed and is currently run at Texas A&M University, along with many other institutions. If you are interested in participating, please email us - ecoliwiki@gmail.com.

This page is to help CACAO students use with/from correctly.

Annotation with some evidence codes will bring up a new field where you must enter something in the with/from field. The table below describes whether with/from is needed and what information is allowed. Note this documentation includes evidence codes that are not usually allowed in CACAO.

Evidence	allowable with/from contents (from documentation, not comprehensive)	mandatory?	ID types currently in use*
EXP	none	-	gene
IDA	none	-	gene, protein
IPI	gene, protein, chemical	Y	gene, protein, peptide, enzyme, chemical, pathway, nucleotide, GO, domain, family, compound, gene symbol, chemical structure
IMP	allele		gene, protein, genotype, morpholino, gene symbol, GO, protein family, literature, RNAi, phenotype, transgene, variation
IGI	gene		feature, protein, gene, genotype, morpholino, gene symbol, peptide, pathway, nucleotide, RNAi, variation, controlled vocabulary
IEP			chemical, gene
ISS	protein, gene, sequence model/method	Y (when known)	gene, protein, peptide, sequence model, gene symbol, pathway, nucleotide, protein, transcript, GO, literature, domain, family, disease, protein family tree, protein structure, motif, site, RNAi, variation
ISO	protein, gene	Y	gene, protein, nucleotide, domain, family
ISA	protein, gene	Y	gene, protein, transcript, feature, nucleotide, domain, gene symbol, protein family, RNAi, variation
ISM	sequence model/method	Y (when known)	gene, protein, sequence model, domain, protein family, protein family tree, protein structure, literature
IGC	gene, pathway		gene, protein, pathway, domain
IBA			gene, protein, protein family tree
IBD			none
IKR	domain, family, annotation rule, alignment, protein family tree		gene, protein, nucleotide, protein family tree
IRD			gene, protein family tree
RCA			gene, protein, domain, protein family, peptide
TAS			gene
NAS			protein
IC	GO	Y	gene, protein, feature, sequence model, GO, domain, protein family, literature
ND			none
IEA	gene, protein, enzyme, sequence model/method, domain, family, controlled vocab. mapping, annotation rule	Y	gene, protein, sequence model, enzyme, transcript, annotation rule, domain, protein family, pathway, controlled vocabulary
edit table

ID types

The content of the with/from field should be an accession to an entity in another database.

Note that when using with for evidence based on homology (ISS, ISA or ISO), the entity in the with/from field must be something that has been experimentally annotated.