Ten Quick Tips for Using the Gene Ontology by Judith A. Blake.
From the post:
The Gene Ontology (GO) provides core biological knowledge representation for modern biologists, whether computationally or experimentally based. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Although extensively used in data analysis workflows, and widely incorporated into numerous data analysis platforms and applications, the general user of GO resources often misses fundamental distinctions about GO structures, GO annotations, and what can and can not be extrapolated from GO resources. Here are ten quick tips for using the Gene Ontology.
Tip 1: Know the Source of the GO Annotations You Use
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Tip 2: Understand the Scope of GO Annotations
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Tip 3: Consider Differences in Evidence Codes
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Tip 4: Probe Completeness of GO Annotations
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Tip 5: Understand the Complexity of the GO Structure
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Tip 6: Choose Analysis Tools Carefully
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Tip 7: Provide the Version of the Data/Tools Used
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Tip 8: Seek Input from the GOC Community and Make Use of GOC Resources
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Tip 9: Contribute to the GO
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Tip 10: Acknowledge the Work of the GO Consortium
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See Judith’s article for her comments and pointers under each tip.
The take away here is that an ontology may have the information you are looking for, but understanding what you have found is an entirely different matter.
For GO, follow Judith’s specific suggestions/tips, for any other ontology, take steps to understand the ontology before relying upon it.
I first saw this in a tweet by Stephen Turner.