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The check list, accessible at any time, reports any missing annotation, in particular required protocols currently undefined in the project.
User feedback: FuncBase is governed by the philosophy that annotation in general and predictive annotation in particular is a work in progress, and that users will often bring domain knowledge that supersedes current or predicted annotation.
However, they should converge on the more generic levels of annotation, in particular with respect to most of the UniGene gene symbol annotations of the genes in our analysis; in our analysis, we study mouse genes.
This effort included initial work on the individual vertebrate anatomy ontologies (prior to their merge into Uberon) to make terms, definitions and relations broadly applicable to the taxa under annotation (in particular, archosaurs and amphibians) and, post-merge, resulted in the addition of 243 anatomical terms (primarily fin, limb and girdle terms) to Uberon.
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We found there was good inter-annotator agreement on the basic entity annotations, in particular when some relaxation of annotation boundaries is permitted, and good agreement on most relation annotations.
Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes.
GO annotations in particular proved difficult to produce at high precision.
Apparently, to make full use of biological knowledge to gain power for a pathway-based analysis, we need knowledge bases with high-resolution annotations, in particular for analysis of next-generation sequencing (NGS) data.
While the survey demonstrated the highest mean value (3.95) and a relatively small deviation (1.00) in opinion, we think the survey is limited in having follow up questions about video annotation tools in particular, and newer technologies in general.
Thirdly, the occurrence of particular pathways in data such as that of Table 1 depends on pathway annotation, and in particular on pathway size.
To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously.
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