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The Gene Ontology Handbook

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Cover of 'The Gene Ontology Handbook'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Primer on Ontologies
  3. Altmetric Badge
    Chapter 2 The Gene Ontology and the Meaning of Biological Function
  4. Altmetric Badge
    Chapter 3 Primer on the Gene Ontology
  5. Altmetric Badge
    Chapter 4 Best Practices in Manual Annotation with the Gene Ontology
  6. Altmetric Badge
    Chapter 5 Computational Methods for Annotation Transfers from Sequence
  7. Altmetric Badge
    Chapter 6 Text Mining to Support Gene Ontology Curation and Vice Versa
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    Chapter 7 How Does the Scientific Community Contribute to Gene Ontology?
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    Chapter 8 Evaluating Computational Gene Ontology Annotations
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    Chapter 9 Evaluating Functional Annotations of Enzymes Using the Gene Ontology
  11. Altmetric Badge
    Chapter 10 Community-Wide Evaluation of Computational Function Prediction
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    Chapter 11 Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools
  13. Altmetric Badge
    Chapter 12 Semantic Similarity in the Gene Ontology
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    Chapter 13 Gene-Category Analysis
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    Chapter 14 Gene Ontology: Pitfalls, Biases, and Remedies
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    Chapter 15 Visualizing GO Annotations
  17. Altmetric Badge
    Chapter 16 A Gene Ontology Tutorial in Python
  18. Altmetric Badge
    Chapter 17 Annotation Extensions
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    Chapter 18 The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations
  20. Altmetric Badge
    Chapter 19 Complementary Sources of Protein Functional Information: The Far Side of GO
  21. Altmetric Badge
    Chapter 20 Integrating Bio-ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes
  22. Altmetric Badge
    Chapter 21 The Vision and Challenges of the Gene Ontology
Attention for Chapter 11: Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (89th percentile)

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Chapter title
Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools
Chapter number 11
Book title
The Gene Ontology Handbook
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-3743-1_11
Pubmed ID
Book ISBNs
978-1-4939-3741-7, 978-1-4939-3743-1
Authors

Monica Munoz-Torres, Seth Carbon

Editors

Christophe Dessimoz, Nives Škunca

Abstract

The Gene Ontology Consortium (GOC) produces a wealth of resources widely used throughout the scientific community. In this chapter, we discuss the different ways in which researchers can access the resources of the GOC. We here share details about the mechanics of obtaining GO annotations, both by manually browsing, querying, and downloading data from the GO website, as well as computationally accessing the resources from the command line, including the ability to restrict the data being retrieved to subsets with only certain attributes.

X Demographics

X Demographics

The data shown below were collected from the profiles of 14 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 1 4%
Israel 1 4%
Unknown 25 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 8 30%
Student > Master 4 15%
Student > Ph. D. Student 4 15%
Student > Bachelor 3 11%
Student > Doctoral Student 2 7%
Other 2 7%
Unknown 4 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 8 30%
Agricultural and Biological Sciences 7 26%
Medicine and Dentistry 2 7%
Mathematics 1 4%
Pharmacology, Toxicology and Pharmaceutical Science 1 4%
Other 1 4%
Unknown 7 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 December 2016.
All research outputs
#4,198,179
of 25,056,530 outputs
Outputs from Methods in molecular biology
#1,046
of 14,096 outputs
Outputs of similar age
#77,552
of 432,184 outputs
Outputs of similar age from Methods in molecular biology
#115
of 1,084 outputs
Altmetric has tracked 25,056,530 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 14,096 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done particularly well, scoring higher than 92% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 432,184 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 1,084 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 89% of its contemporaries.