AceDB classes tutorial

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The following table lists common WormBase classes.

Object Name Class Notes
A Predicted Gene A cosmid dot name, such as F59E12.2 Predicted_Gene A class name of "Sequence" is also recognized.
A Named Gene A three letter name, such as zyg-1 Locus
A Genbank Accession Number (protein or nucleotide) The accession number Accession_Number This will retrieve an Accession_Number object, which is a list of WormBase names that correspond to that accession number.
A Protein A wormpep accession number, proceeded by "WP:", as in WP:CE28571 Protein
A Clone The cosmid or YAC name, for example F59E12 Clone
Genomic Sequence The cosmid or YAC name from which the sequence was made, for example F59E12 Genomic_Sequence A class name of "Sequence" is also recognized.
A GenePair The Research Genetics name, preceded by the prefix "sjj_" (for Steve Jones, who designed the pairs). For example, sjj_F59E12.2. PCR_Product
A Cell A cell name, such as ADAR; notice that paired cells, such as ADAR and ADAL are treated separately Cell
A Protein Family

The accession number, proceeded by the database name.

Examples include the Interpro family INTERPRO:IPR000039, the

Prosite motif PS:PS00041, and the PFAM family PFAM:PF00352
Motif
An RNAi Experiment

The accession number of the experiment. This is typically the name

of the overlapping gene preceded by the laboratory prefix. For example, an RNAi experiment that covers gene F59E12.2 and was performed in Julie

Ahringer's lab (JA), will have the name JA:59E12.2
RNAi