Initial set of gene ontology (GO) terms for the D v virgifera GCF_003013835.1 RefSeq protein models

dataset

posted on 2024-02-16, 22:29 authored by Brad CoatesBrad Coates

Gene ontologies generated using GOanna with a standard pipeline (https://agbase-docs.readthedocs.io/en/latest/goanna/using_goanna_cmd.html ; default settings) with queries against the invertebrate subsection of the UniProt database. Alignments provided in html format. The initial set of gene ontology (GO) terms in the sliminput.txt files generated by GOanna were used as input for GOSlimViewer to parse and summarize molecular function (F), biological process (P) and cellular component (C) at level 2. Annotations were also converted to gene annotation format (.gaf) file using Goanna2ga.

Resources in this dataset:

Resource Title: Alignment of Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models against invertebrate proteins in the UniProt database .

File Name: Dvir_2.0GOAnna.align.sn060d1588083909.html
Resource Description: Gapped BLAST and PSI-BLAST results for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models against 22,595 invertebrate protein sequences in the UniProt database at AgBase (invertebrates_exponly.fa)
Resource Software Recommended: GOanna,url: https://agbase.arizona.edu/cgi-bin/tools/GOanna.cgi

Resource Title: Summary of all putative GO annotations received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models.

File Name: Dvir_2.0_GOAnna_GOs.sn060d1588083909.txt
Resource Description: Putative GO annotations received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models. Contains all putative hit with proteins in a curated UniProt invertebrate database, invertebrates_exponly.fa, maintained at AgAbase (https://agbase.arizona.edu/cgi-bin/team.pl)
Resource Software Recommended: GOanna,url: https://agbase.arizona.edu/cgi-bin/tools/GOanna.cgi

Resource Title: Annotations used for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models.

File Name: Dvir_2.0_GOAnna_ProtAnnotations_sn060d1588083909.txt
Resource Description: Top annotation received for each Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models. Contains only the "top" hit with proteins in a curated UniProt invertebrate database, invertebrates_exponly.fa, maintained at AgAbase (https://agbase.arizona.edu/cgi-bin/team.pl). Carried through for analyses using GOslim.
Resource Software Recommended: GOanna,url: https://agbase.arizona.edu/cgi-bin/tools/GOanna.cgi

Resource Title: Putative GO annotations received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models reformatted for GOslim input.

File Name: Dvir_2.0_GOAnna_sliminput_sn060d1588083909.txt
Resource Description: Putative GO terms received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models.

Resource Title: Summary of GO biological process (BP) terms received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models.

File Name: Dvir_2.0GOslimout.bp.w63fq51588102929.bp_.txt
Resource Software Recommended: GOslimViewer,url: https://agbase.arizona.edu/cgi-bin/tools/goslimviewer_select.pl

Resource Title: Summary of GO cellular component (CC) terms received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models..

File Name: Dvir_2.0GOslimoutcc.w63fq51588102929.cc.txt
Resource Software Recommended: GOslimViewer,url: https://agbase.arizona.edu/cgi-bin/tools/goslimviewer_select.pl

Resource Title: Summary of GO molecular function (MF) terms received for Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models..

File Name: Dvir_2.0_GOslimoutmf.w63fq51588102929.txt
Resource Software Recommended: GOslimViewer,url: https://agbase.arizona.edu/cgi-bin/tools/goslimviewer_select.pl

Resource Title: Gene annotation file (.gaf) output generated for GO terms assigned to Diabrotica virgifera virgifera RefSeq GCF_003013835.1 protein models..

File Name: GOanna2GA_Reformat_kky33f1592832838.xls
Resource Software Recommended: GOanna2ga,url: https://agbase.arizona.edu/cgi-bin/tools/GOanna2ga.cgi

Funding

USDA-NIFA: 2010-04160

USDA-ARS: 5030-22000-019-00D

History

Data contact name

Coates, Brad

Data contact email

brad.coates@usda.gov

Publisher

Ag Data Commons

Intended use

The gene ontologies provide putative functional information for the Diabrotica virgifera virgifera RefSeq GCF_003013835.1 gene models which may assist in biological interpretation of gene function in downstream experiments.

Use limitations

GO annotations are descriptions of putative gene function(s) obtained from homologies to proteins from related species. These putative functions have not been validated and should be interpreted with caution.

Temporal Extent Start Date

2021-03-17

Frequency

notPlanned

Theme

Not specified

Geographic Coverage

{"type":"FeatureCollection","features":[{"geometry":{"type":"Point","coordinates":[-93.647443771624,42.030300694796]},"type":"Feature","properties":{}},{"geometry":{"type":"Point","coordinates":[-93.646267890963,42.030234250882]},"type":"Feature","properties":{}}]}

Geographic location - description

Ames, Iowa, United States

ISO Topic Category

biota
farming

Ag Data Commons Group

AgBioData

National Agricultural Library Thesaurus terms

genes; models; invertebrates; gene ontology; Diabrotica virgifera virgifera; proteins; rootworms

OMB Bureau Code

005:18 - Agricultural Research Service

OMB Program Code

005:040 - National Research

ARS National Program Number

Pending citation

Public Access Level

Public

Preferred dataset citation

Coates, Brad S. (2022). Initial set of gene ontology (GO) terms for the D v virgifera GCF_003013835.1 RefSeq protein models. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1524777

Usage metrics

Keywords

Gene ontology GOanna Diabrotica virgifera virgifera NP304 data.gov ARS

Licence

U.S. Public Domain

Exports

RefWorks

BibTeX

Ref. manager

Endnote

DataCite

NLM