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GOMAP

Gene Ontology Meta Annotator for Plants

GOMAPMaking a genome sequence accessible and useful involves three basic steps: genome assembly, structural annotation, and functional annotation. The quality of data generated at each step influences the accuracy of inferences that can be made, with high- quality analyses produce better datasets resulting in stronger hypotheses for downstream experimentation.

PhenotypeGene Ontology Meta Annotator for Plants (GOMAP) is a high-throughput pipeline to annotate GO terms to plant protein sequences in a high-confidence and reproducible manner. It combines sequence-similarity, domain-presence and mixed-method based approaches and we are currently applying it to the reference genomes of several agriculturally important plants (maize, wheat, rice, cotton, soybean). All generated annotation datasets as well as the source code are publicly available.

For more information on how the pipeline works as well as instructions on how to run it yourself, please check out the documentation on GitHub.

GOMAP was developed from maize-GAMER (Publication), a collaborative project to improve the status of gene functional annotation in maize.

© 2018 Dill-PICL, Iowa State University

 


Maize-GAMER

maize-GAMER is a collaborative project to improve the status of gene functional annotation in maize. The project has three main areas of focus, namely

  1. Design a pipeline for the functional annotation of maize genes.
  2. Use manually curated test data to evaluate the annotations and generate a best subset of annotations for use
  3. Design a user friendly review system for the community to provide feedback and endorsements of the annotations

 

Predicting Annotations

Annot PipelineGO annotations are generated using three different approaches in the pipeline.

  1. Sequence similarity to Arabidopsis (TAIR) and existing plant genes with curated GO annotations.
  2. InterproScan to detect protein domains which have GO terms annotated to them.
  3. CAFA (Critical Assessment of Functional Annotation) tools (Argot2, FANNGO, PANNZER) that use a combination of machine learning and statistics to predict GO terms for input genes

These annotations will be compared to available GO annotations for maize from Gramene. Gramene uses the Ensembl Compara pipeline to generate GO annotations. RBH – Reciprocal Best Hit

 

 

 

 

Evaluating Annotations

Eval Pipeline

Represents the part of the pipeline which is used to evaluate the annotations by calculating and comparing the performance measures.

  1. Test datasets is comprised of Gold Standard - manually curated annotations from MaizeGDB. About 4% of the maize protein coding genes are represented in this test dataset.
  2. Protein-centric evaluation metrics from the CAFA project are currently being used to evaluate different tools.
    • Precision (PR) is the mean of the proportion of correctly predicted annotations for a given protein compared to the total number of predictions
    • Recall (RC) is the mean proportion of correctly predicted annotations for a given protein compared to the total number of annotations in the test dataset for the given protein.
    • F-score is a single value which reflects a tool’s accuracy, and is calculated from RP and RC

 

Reviewing Annotations

Review PipelineRepresents the outline of the Review system which will be implemented at the end of evaluation step.

  1. Basic View will have minimal information necessary for subject experts to review their gene(s) of their choice quickly.
  2. Evidence View will allow users to look at the tools that support a particular GO annotation. Each tool supporting the particular annotation will have a simple graphic showing the details of the annotations. E.g., Sequence similarity based methods will have a simple diagram representing the representative target, coverage, identity, and E-value of a given BLAST hit.

All this data will be made available for download for downstream analysis of you own experiments. Non-reviewed annotations will be made available as soon as the evaluation of the results from the pipeline are completed. Reviewed annotations will be made available after the release of the tool to the maize community and sufficient time has been given for accumulation of community effort for revision of the Non-reviewed annotations.


People

Principal Investigator

Carolyn J. Lawrence-DillCarolyn Dill

Associate Professor

GDCB, BCB & Agronomy Iowa State University

triffid@iastate.edu

 

Support Staff

Darwin CampbellDarwin Campbell

Database Manager

Dill PICL Iowa State University

darwin@iastate.edu

 

Scott ZarecorScott Zarecor

Programmer

Dill PICL Iowa State University

szarecor@iastate.edu

 

 

Students

Gokul WimalanathanGokul Wimalanathan

Doctoral Candidate

BCB Dill PICL & Vollbrecht Lab Iowa State University

kokul@iastate.edu

 

Dennis PsaroudakisDennis Psaroudakis

Fulbright scholar

Dill PICL Iowa State University

dpsaroud@iastate.edu

 

Collaborators

Carson AndorfCarson Andorf

Director

MaizeGDB UDSA - ARS

 

 

Iddo FriedbergIddo Friedberg

Associate Professor

VMPM & BCB Iowa State University

 

 

Alumni

Chris LawrenceChris Lawrence

Undergraduate

Senior Genetics Dill PICL Iowa State University

 

 


Datasets

Publicly available GOMAP Datasets

These datasets generated by GOMAP are new high-coverage and reproducible functional annotation sets of protein coding genes based on Gene Ontology (GO) term assignments. Follow the DOI link for more information, access, and download. Check out the main project page (Home on the left) to find out more about how they were generated and how you can use the pipeline yourself.

Rel Species Germplasm/
Line
Assembly/
Annotation
DOI
(link)
Data Wrangler
2022 Humulus lupulus (Common Hop) Cascade HopBase 10.25739/ew58-8d76 Leila Fattel
2022 Zea mays (Maize) B73 Zm-B73-REFERENCE-NAM-5.0 10.25739/g1rt-b278 Olivia Johnson
2022 Capsicum annuum (Pepper) cv CM334 Pepper Genome Platform (PGP) 10.25739/cqn7-yt96 Leila Fattel
2021 Camellia sinensis
(Tea)
sinensis TPIA CSS_ChrLev_20200506 10.25739/w1fz-9313 Leila Fattel
2021 Vaccinium corymbosum L.
(Highbush Blueberry)
Draper GigaDB V_corymbosum_v1.0 10.25739/q7rq-e992 Leila Fattel
2021 Brassica napus
(Canola)
ZS11 BnPIR ZS11 genome 10.25739/xgmr-hr31 Dollye Starr
2021 Coffea canephora
(Coffee)
Coffea canephora CGH C. canephora genome v1.0 10.25739/rm4j-3580 Leila Fattel
2021 Solanum pennellii
(Tomato)
Solanum pennellii Bolger2014.v1 10.25739/fhr4-cx67 Dennis Psaroudakis
2021 Solanum lycopersicum
(Tomato)
Heinz 1706 ITAG4.1 10.25739/zh2v-4p15 Dennis Psaroudakis
2021 Musa acuminata
(Banana)
DH-Pahang NCBI ASM31385v2 10.25739/yt7w-gs55 Leila Fattel
2021 Theobroma cacao
(Cacao)
B97-61/B2 NCBI Criollo_cocoa_genome_V2 10.25739/9qc0-n310 Leila Fattel
2021 Vitis vinifera
(Grape)
Pinot Noir
PN40024
Genoscope 2010 genome 12X 10.25739/jtfk-q888 Haley Dostalik
2020 Pinus lambertiana
(Sugar Pine)
Sugar Pine TreeGenesDB sugar pine assembly v1.5 10.25739/jvs4-xr88 Colleen Yanarella
2020 Cannabis sativa
(Cannabis)
Hemp NCBI Cannabis sativa GCA_900626175.1 10.25739/ab9z-2z86 Kevin Chiteri
2020 Gossypium raimondii
(Cotton)
Cotton D Gossypium raimondii JGI v2.1 10.25739/a13t-zh47 Parnal Joshi
2019 Glycine max (Soybean) Williams 82 Joint Genome Institute (JGI) Glycine max genome assembly Wm82.a4.v1 (genotype Williams 82, assembly 4.0, gene model annotation 1.0) 10.25739/59ec-1719 Dennis Psaroudakis
2019 Oryza sativa (Rice) japonica IRGSP 1.0 10.25739/53g0-j859 Ha Vu
2019 Triticum aestivum (Wheat) Chinese Spring IWGSC's RefSeq 1.1 10.25739/65kf-jz20 Dennis Psaroudakis
2019 Zea mays (Maize) Mo17 Zm-Mo17-REFERENCE-CAU-1.0 10.25739/m634-cn58 Kokulapalan Wimalanathan
2019 Zea mays (Maize) PH207 Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0 10.25739/dm9s-aa15 Kokulapalan Wimalanathan
2019 Zea mays (Maize) W22 Zm-W22-REFERENCE-NRGENE-2.0 Zm00004b.1 10.25739/e4va-9f09 Kokulapalan Wimalanathan
2019 Hordeum vulgare (Barley)   IBSC_PGSB_r1 10.25739/zvgv-8e37 Colleen Yanarella
2019 Brachypodium distachyon (Stiff Brome) Bd21 Bd21.v3.1.r1 10.25739/dw2t-3g82 Kokulapalan Wimalanathan
2019 Sorghum bicolor (Sorghum) BTx623 BTx623.v3.0.1.r1 10.25739/4ty0-ye98 Kokulapalan Wimalanathan
2019 Arachis hypogaea (Peanut) Tifrunner Arachis hypogaea assembly 1.0 10.25739/chab-0e35 Dennis Psaroudakis
2019 Medicago truncatula (Barrel Clover) R108_HM340 R108: v1.0 10.25739/2sqc-j140 Dennis Psaroudakis
2019 Medicago truncatula (Barrel Clover) A17_HM341 Mt4.0v2 10.25739/py38-yb08 Dennis Psaroudakis
2019 Phaseolus vulgaris (Common Bean) G19833 DOE-JGI and USDA-NIFA Phaseolus vulgaris
annotation 2.0
10.25739/1ywe-ew96 Dennis Psaroudakis
2019 Vigna unguiculata (Cowpea) IT97K-499-35 JGI annotation v1.1 10.25739/cdx9-wr97 Dennis Psaroudakis
2017 Zea mays (Maize) B73 RefGen_v3 5b+ 10.7946/P2S62P Kokulapalan Wimalanathan
2017 Zea mays (Maize) B73 RefGen_V4 Zm00001d.2 10.7946/P2M925 Kokulapalan Wimalanathan