RA conceived and coordinated the study, extracted total RNA, participated in bioinformatic analyses, carried out manual processing of the data, annotation of miRNAs and submissions to miRBase and GeneBank and drafted the manuscript.
The use of the ML model substantially reduced the need for manual chart reviews and overall data annotation effort (approximately twofold).
The annotations of the assembled genome sequences of C. ulcerans 809 and C. ulcerans BR-AD22 were performed with the GenDB system that supports automatic annotation strategies and manual data curation [ 27].
The annotation tool provides manual data entry and query on de-identified information obtained from these questionnaires through a "point and click" interface that internally integrates with annotated clinicopathology data sources.
To expedite the splice site annotation process we developed, using PHP [ 41] and MySQL [ 42], a web interface which allowed for manual data curation.
Manual annotation data is stored in a separate MySQL database.
For example, GO_REF 0000024 (http://www.geneontology.org/cgi-bin/references.cgi GO_REF 0000024), titled 'Manual transfer of experimentally verified manual GO annotation data to orthologs by curator judgment of sequence similarity', was created to describe the transfer of manual annotations using curator judgment to annotations associated with the ISS code.org/cgi-bin/references.cgi GO_REF 0000024
Besides the (limited) manual annotation data sets, we created additional training data from existing curated data in the CTD-Pfizer collaboration [10] where the raw data contains 88,000 articles with document-level annotations of drug-disease and drug-phenotype interactions.
In AmiGO, the GOC browser, the GO term records clearly show the number of proteins annotated with that term by all GOC databases, however the protein records only include manual annotation data.
The ability to capture in a manual GO annotation contextual data for a protein's functional roles, such as cell and tissue type or organism developmental stage, will be a great added benefit to future analyses of datasets.
