An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

from A critical assessment of text mining methods in molecular biolog

AgBase: a functional genomics resource for agriculture

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms

The impact of focused Gene Ontology curation of specific mammalian systems.

The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome. AVAILABILITY: GO ANNOTATION DATA IS FREELY AVAILABLE FROM: ftp://ftp.geneontology.org/pub/go/gene-associations

Transcriptomic analyses of murine resolution-phase macrophages

Macrophages are either classically (M1) or alternatively-activated (M2). While this nomenclature was generated from monocyte-derived macrophages treated in vitro with defined cytokine stimuli, the phenotype of in vivo-derived macrophages is less understood. We completed Affymetrix-based transcriptomic analysis of macrophages from the resolution-phase of a zymosan-induced peritonitis. Compared to macrophages from hyper-inflamed mice possessing a pro-inflammatory nature as well as naive macrophages from the un-inflamed peritoneum, resolution-phase macrophages (rM) are similar to monocytes-derived dendritic cells (DC), being CD209a positive but lack CD11c. They are enriched for antigen processing/presentation (MHC-II [H2-Eb1, H2-Ab1, H2-Ob, H2-Aa], CD74, CD86), secrete T- and B-lymphocyte chemokines (Xcl1, Ccl5, Cxcl13) as well as factors that enhance macrophage/DC development and promote DC/T cells synapse formation (Clec2i, Tnfsf4, Clcf1). rM are also enriched for cell cycle/proliferation genes as well as Alox15, Timd4 and Tgfb2, key systems in the termination of leukocyte trafficking and clearance of inflammatory cells. Finally, comparison with in vitro-derived M1/M2 shows that rM are neither classically nor alternatively activated but possess aspects of both definitions consistent with an immune regulatory phenotype. We propose that macrophage in situ cannot be rigidly categorised as they can express many shades of the inflammatory spectrum determined by tissue, stimulus and phase-of-inflammation

Showing GO annotation of 'kinase activity' GO:0016301 (right tool bar) by user 9-1 with supporting text evidence (central panel)

<p><b>Copyright information:</b></p><p>Taken from "An evaluation of GO annotation retrieval for BioCreAtIvE and GOA"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 1):S17-S17.</p><p>Published online 24 May 2005</p><p>PMCID:PMC1869009.</p><p></p> The left tool bar shows the UniProt accession number, in this case Q8IWU2 has been annotated. Q8IWU2 represents a KPI-2 protein so the user has been evaluated based on the evidence text as 'high' for GO term prediction and 'high' for representing the correct gene product. The user also uses this sentence to predict the GO term 'receptor signaling protein serine/threonine kinase activity'(GO:0004702). Although that GO annotation is correct for this protein the evidence text supplied does not support that level of detail. The same evidence text was evaluated as 'general' for the GO term prediction of GO:0004702 (same lineage as correct GO term 'kinase activity') and 'high' for representing the correct gene product

AgBase: a functional genomics resource for agriculture

Abstract Background Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. Description To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. Conclusion The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.</p