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Questions tagged [terminology]

Nomenclature. Questions relating to conventions, definitions, word usage.

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Is there a standard API for terminology services?

I'm looking for a standard to access terminology services. A terminology service provides an generalized API to multiple terminologies like ICD10, MedDRA, Snomed, Loinc etc. But I'm looking for a ...
witchi's user avatar
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1 vote
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Single-cell RNA sequencing proper abbreviation [closed]

I wonder which form of a single-cell RNA sequencing abbreviation is correct: scRNA-seq scRNA-Seq In the same single-cell sequencing Wikipedia article, both forms appear. There is also inconsistency ...
maciejwww's user avatar
  • 215
2 votes
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Knowing which positions are variants

Let's say I'm sequencing a donor, and I have 20X coverage. And let's say all the reads covering a particular base has the same allele at the position. Then, is that position considered a "variant" ...
Jonathan's user avatar
  • 341
14 votes
1 answer

What is the difference between a Bioinformatics pipeline and workflow?

I want to understand the difference between pipeline systems and workflow engines. After reading A Review of Scalable Bioinformatics Pipelines I had a good overview of current bioinformatics ...
A.Dumas's user avatar
  • 487
6 votes
1 answer

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...
Zheng Keong Ng's user avatar
2 votes
1 answer

What is a site in a phylogenetic tree?

When I read about a term related to phylogenetics, for example, $K_a$/$K_s$ ratio, I constantly see the word site, whose meaning isn't explained and it puzzles me. For example substitutions per ...
banan3'14's user avatar
  • 123
1 vote
1 answer

What does "ALT+ cancer cells", the plus sign mean?

In many scientific papers, there is a plus sign: ... T-circles have also been detected in ALT+ (telomerase-negative) cells9 and ... What does the "+" mean? Does it mean differentially expressed?
ABCD's user avatar
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5 votes
2 answers

Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?

For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence). For real-...
Rebecca J. Stones's user avatar
6 votes
1 answer

What is the difference between SAM mapping quality and Blast E-value?

Blast reports E-values, but short-read mappers report mapping qualities. Are they the same thing? Can they be converted to each other? If not, why blast doesn't report mapping quality while short-read ...
medbe's user avatar
  • 777
7 votes
3 answers

What is the difference between NGS, 2GS, SBS and HTS?

I've come across a bit of confusion about the initialism NGS, so think it would be a good idea to clarify this term (and similar terms like 2GS, SBS, and HTS) for this site with a bit of discussion. ...
gringer's user avatar
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6 votes
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Difference between computational biology, bioinformatics and biostatistics [closed]

I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...
Scott Gigante's user avatar
4 votes
3 answers

Bootstrap analysis - why it is called bootstrap?

Bootstrap analysis, bootstrapping etc are quite common jargons of bioinformatics and phylogenetics. However, it is not very much clear to us, what exactly being meant by "a boot's straps". Does it ...
Always Confused's user avatar