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

Metadata Updated: May 2, 2024

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.htmlResource 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.txtResource 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.txtResource 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.txtResource 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_.txtResource 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.txtResource 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.txtResource 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.xlsResource Software Recommended: GOanna2ga,url: https://agbase.arizona.edu/cgi-bin/tools/GOanna2ga.cgi

Access & Use Information

Public: This dataset is intended for public access and use. License: us-pd

Downloads & Resources

Dates

Metadata Created Date April 10, 2024
Metadata Updated Date May 2, 2024
Data Update Frequency irregular

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date April 10, 2024
Metadata Updated Date May 2, 2024
Publisher Agricultural Research Service
Maintainer
Identifier 10.15482/USDA.ADC/1524777
Data Last Modified 2024-02-16
Public Access Level public
Data Update Frequency irregular
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 9e5ec736-6f3c-43f7-b6be-dc88f83f3216
Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
Harvest Source Title USDA JSON
License https://www.usa.gov/publicdomain/label/1.0/
Old Spatial {"type": "MultiPoint", "coordinates": -93.647443771624, 42.030300694796, -93.646267890963, 42.030234250882}
Program Code 005:040
Source Datajson Identifier True
Source Hash b3fefe2655f55eb277ee15ce97df80d52429492ac13d48c65330b26eb7515af9
Source Schema Version 1.1
Spatial {"type": "MultiPoint", "coordinates": -93.647443771624, 42.030300694796, -93.646267890963, 42.030234250882}

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