Evidence map›Paper›PMID 34627149›Full record

ArticleBMC genomics2021

Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes.

Matthew R Lueder, Regina Z Cer, Miles Patrick, Logan J Voegtly, Kyle A Long, Gregory K Rice, Kimberly A Bishop-Lilly

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Matthew R LuederGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Regina Z CerGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Miles PatrickMount St. Mary's University, Emmitsburg, MD, USA.
Logan J VoegtlyGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Kyle A LongGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Gregory K RiceGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.
Kimberly A Bishop-LillyGenomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA. Kimberly.a.bishop-lilly.civ@mail.mil.ORCID http://orcid.org/0000-0002-5744-8493

Funding

DOD Peer Reviewed Medical Research Program (US) PR182667U.S. Navy WUN A1417
6 · The paper itself

Abstract

backgroundFunctional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Manual annotation efforts are time-consuming and complex; however, software can help reduce these drawbacks.

resultsWe created Manual Annotation Studio (MAS) to improve the efficiency of the process of manual functional annotation prokaryotic and viral genomes. MAS allows users to upload unannotated genomes, provides an interface to edit and upload annotations, tracks annotation history and progress, and saves data to a relational database. MAS provides users with pertinent information through a simple point and click interface to execute and visualize results for multiple homology search tools (blastp, rpsblast, and HHsearch) against multiple databases (Swiss-Prot, nr, CDD, PDB, and an internally generated database). MAS was designed to accept connections over the local area network (LAN) of a lab or organization so multiple users can access it simultaneously. MAS can take advantage of high-performance computing (HPC) clusters by interfacing with SGE or SLURM and data can be exported from MAS in a variety of formats (FASTA, GenBank, GFF, and excel).

conclusionsMAS streamlines and provides structure to manual functional annotation projects. MAS enhances the ability of users to generate, interpret, and compare results from multiple tools. The structure that MAS provides can improve project organization and reduce annotation errors. MAS is ideal for team-based annotation projects because it facilitates collaboration.

Indexed as

Databases, GeneticGenome, MicrobialDatabases, ProteinGenome, ViralSoftwareBioinformaticsFunctional annotationGene annotationGenome annotationHigh-performance computingManual annotationMicrobial genomicsPhagePhage annotation

Identifiers

PMID34627149
PMCPMC8501643

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.