We tested the BioSQL schema, but it did not precisely fit to our needs, mainly because our annotation entities refer to three other entities (qualifying note n, object o and the annotation method m).
An example of annotation is the following: if an annotation method m associates a CDS c to an EC number e with a score s, we create a SubseqDBxRefAnnotation object with the following attributes: method = m, object o = subsequence of c, qualifying note n = e, score = s and parent = null.
and some in controlled vocabulary ("Subcellular location", "Catalytic activity", etc).. Most controlled vocabulary subsections can contain a free text "Note =" that allows to qualify the annotation and provides additional information.
When the TF is presented in any of the variants (ii v), the EMSA qualifies for annotation of a GO term for 'specific DNA binding'.
For the details of the clausal unit qualified for the annotation, please see the Appendix (Additional file 1).
The lengths of the assembled unigenes ranged from 90 to 7641 bp (Additional file 1).> The GetORF tool from EMBOSS [ 32] was used for gene prediction, which identified all of the assembled contigs and isotigs to encode protein sequences and were qualified for further annotation.
In accordance with the overall guidelines for GO annotations, each DbTF annotation must be qualified with an evidence code indicating how the annotation is supported by experimental evidence (http://www.geneontology.org/GO.evidence.shtml).shtml
As in Table 2, queries were qualified by Medical Subject Headings (MeSH) annotation to minimize spurious associations.
Queries were qualified by Medical Subject Headings (MeSH) annotation to minimize spurious associations.
Then, human UniGene IDs corresponding to Affymetrix IDs for qualified genes were obtained using annotation file downloaded from the Affymetrix website (34097 ID).
