Terminology

CodeSystem:repositoryType

Type for access of external URI.
CodeDisplayDefinition
directlinkClick and seeWhen URL is clicked, the resource can be seen directly (by webpage or by download link format).
openapiThe URL is the RESTful or other kind of API that can access to the result.When the API method (e.g. [base_url]/[parameter]) related with the URL of the website is executed, the resource can be seen directly (usually in JSON or XML format).
loginResult cannot be access unless an account is logged inWhen logged into the website, the resource can be seen.
oauthResult need to be fetched with API and need LOGIN( or cookies are required when visiting the link of resource)When logged in and follow the API in the website related with URL, the resource can be seen.
otherSome other complicated or particular way to get resource from URL.Some other complicated or particular way to get resource from URL.

CodeSystem:orientationType

Type for orientation.
CodeDisplayDefinition
senseSense orientation of referenceSeqSense orientation of reference sequence.
antisenseAntisense orientation of referenceSeqAntisense orientation of reference sequence.

CodeSystem:qualityType

Type for quality report.
CodeDisplayDefinition
indelINDEL ComparisonINDEL Comparison.
snpSNP ComparisonSNP Comparison.
unknownUNKNOWN ComparisonUNKNOWN Comparison.

CodeSystem:sequenceType

Type if a sequence -- DNA, RNA, or amino acid sequence.
CodeDisplayDefinition
aaAA SequenceAmino acid sequence.
dnaDNA SequenceDNA Sequence.
rnaRNA SequenceRNA Sequence.

CodeSystem:strandType

Type for strand.
CodeDisplayDefinition
watsonWatson strand of referenceSeqWatson strand of reference sequence.
crickCrick strand of referenceSeqCrick strand of reference sequence.

CodeSystem:chromosome-human

Chromosome number for human.
CodeDisplayDefinition
1chromosome 1chromosome 1.
2chromosome 2chromosome 2.
3chromosome 3chromosome 3.
4chromosome 4chromosome 4.
5chromosome 5chromosome 5.
6chromosome 6chromosome 6.
7chromosome 7chromosome 7.
8chromosome 8chromosome 8.
9chromosome 9chromosome 9.
10chromosome 10chromosome 10.
11chromosome 11chromosome 11.
12chromosome 12chromosome 12.
13chromosome 13chromosome 13.
14chromosome 14chromosome 14.
15chromosome 15chromosome 15.
16chromosome 16chromosome 16.
17chromosome 17chromosome 17.
18chromosome 18chromosome 18.
19chromosome 19chromosome 19.
20chromosome 20chromosome 20.
21chromosome 21chromosome 21.
22chromosome 22chromosome 22.
Xchromosome Xchromosome X.
Ychromosome Ychromosome Y.

ValueSet: chromosome-human

Chromosome number for human.

ValueSet: SNOMEDCTCodesForSpecies

Codes identifying atomic results of observations when value is type codeableConcept. This value set includes all the children of SNOMED CT Concepts from SCTIDs 404684003 Clinical finding (finding), 410607006 Organism (organism),362981000 Qualifier value (qualifier value), 105590001 Substance (substance), and 123037004 Body structure (body structure). It is provided as a suggestive example

ValueSet: FDA-Method

This value set includes sequence quality method

ValueSet: strandType

Type for strand.

ValueSet: ENSEMBL

This value set includes all Reference codes

ValueSet: repositoryType

Type for access of external URI.

ValueSet: qualityType

Type for quality report.

ValueSet: sequenceType

Type if a sequence -- DNA, RNA, or amino acid sequence.

ValueSet: FDA-StandardSequence

This value set includes sequence quality standard

ValueSet: sequenceStatus

Codes providing the status of the variant test result.

ValueSet: orientationType

Type for orientation.

ValueSet: CopyNumberEvent

Copy Number Event.