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AgBase

    [AgBase](https://agbase.arizona.edu/index.html) Version 2.0 is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations. Its long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase uses controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species.

    Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava

      Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.

      Genomes To Fields 2016

        Phenotypic, genotypic, and environment data for the 2016 field season: The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/GenomesToFields_G2F_2016_Data_Mar_2018).

        Genomes To Fields 2015

          Phenotypic, genotypic, and environment data for the 2015 field season: The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Carolyn_Lawrence_Dill_G2F_Mar_2017).

          Genomes To Fields 2014

            Phenotypic, genotypic, and environment data for the 2014 field season: The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Carolyn_Lawrence_Dill_G2F_Nov_2016_V.3).

            Genomes To Fields (G2F) Inbred Ear Imaging Data 2017

              A subset of ~30 inbreds were evaluated in 2014 and 2015 to develop an image based ear phenotyping tool. The data is stored in [CyVerse](http://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Edgar_Spalding_G2F_Inbred_Ear_Imaging_June_2017).

              Maize-GAMER: Maize B73 RefGen_v3 5b+

                This dataset from maize-GAMER is a new high-coverage and reproducible functional annotation of maize (*Zea mays*) protein coding genes based on Gene Ontology (GO) term assignments that covers all genes in the B73 RefGen_v3 5b+ set. Data are compressed gzip (.gz) files.

                Maize-GAMER: GO Annotations, Methods, Evaluation and Review

                  maize-GAMER is a collaborative project to improve the status of gene functional annotation in maize (*Zea mays*). The project has three main areas of focus, namely * Design a pipeline for the functional annotation of maize genes. * Use manually curated test data to evaluate the annotations and generate a best subset of annotations for use * Design a user friendly review system for the community to provide feedback and endorsements of the annotations