Allele Registry 1.01.xx Manual V2
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Allele Registry
versions 1.01.xx
Administrator's manual
document version 2
Table of Contents
Introduction..............................................................................................................................................3
Users privileges.....................................................................................................................................3
Responses in simple text format............................................................................................................4
Alleles Database....................................................................................................................................4
Administrator’s API for managing alleles and external identifiers....................................................5
Import new identifiers...........................................................................................................................5
Request.............................................................................................................................................5
Parameters........................................................................................................................................5
Payload.............................................................................................................................................6
Response...........................................................................................................................................6
Delete all identifiers of given type........................................................................................................7
Request.............................................................................................................................................7
Response...........................................................................................................................................7
Delete alleles by CA/PA IDs.................................................................................................................7
Request.............................................................................................................................................7
Payload.............................................................................................................................................7
Response...........................................................................................................................................7
Administrator’s API for External Sources............................................................................................8
Create new external source....................................................................................................................8
Request.............................................................................................................................................8
Parameters........................................................................................................................................8
Modify existing external source............................................................................................................9
Request.............................................................................................................................................9
Parameters:.......................................................................................................................................9
Delete external source...........................................................................................................................9
Request.............................................................................................................................................9
Assign user to an external source..........................................................................................................9
Request.............................................................................................................................................9
Remove user from an external source...................................................................................................9
Request.............................................................................................................................................9
Unpublished standard API requests.....................................................................................................10
Query all genomic alleles....................................................................................................................10
Request...........................................................................................................................................10
Parameters......................................................................................................................................10
Response.........................................................................................................................................10
Query all protein alleles......................................................................................................................10
Request...........................................................................................................................................10
Parameters......................................................................................................................................10
Response.........................................................................................................................................10
Return basic properties of given reference sequence..........................................................................11
Request...........................................................................................................................................11
Response.........................................................................................................................................11
Match protein and transcript variants for gene mutation.....................................................................11
Request...........................................................................................................................................11
Parameters......................................................................................................................................11
Response.........................................................................................................................................11
Introduction
This document contains description of additional functionality of Allele Registry that is available only
for users with administrator privileges, as well as, some features that are not described in official
documentation available for API users. The document does not repeat information included already in
the API specification.
Users privileges
API requests can be send with or without authentication tokens. The authentication procedure is
described in details in API specification. It is based on Genboree authentication and uses connection to
MySQL Genboree database to verify users credentials. In general, each requests is assigned to one of
the four authorization levels described in the table below.
Authorization
level
Requirements
Access rights
Anonymous
• request without authentication parameters • all GET and POST requests
(gbLogin, gbTime, gbToken)
Authenticated user
• request
with
correct
authentication • all GET and POST requests
parameters (gbLogin, gbTime, gbToken)
• new variants registration
• user assigned to Genboree group “Registry”
Authenticated user • request
with
correct
authentication • all GET and POST requests
assigned
to
parameters (gbLogin, gbTime, gbToken)
• new variants registration
external source
• user assigned to Genboree group “Registry” • adding and removing links
• user assigned to one of external sources
from assigned external
sources
Administrator
• request
with
correct
authentication • all requests
parameters (gbLogin, gbTime, gbToken)
• user assigned to Genboree group “Registry”
• user login set in an array “superusers” in the
configuration file
When Allele Registry is run with the parameter “--no_auth”, authentication parameters are ignored and
all request are authorized on “Administrator” level. In this mode, Allele Registry server can be run
without installed Genboree (wowever, MySQL with “externalSources” database is still required).
Responses in simple text format
All requests returning as a response a single Allele object or an array of Alleles objects support
additional protocol named “txt”. When this protocol is specified in the request, a response contains
simple text file instead of JSON content. The text content consists of two TAB-separated columns, the
first column contains single HGVS expressions (alleles definitions) while the second column contains
CA/PA identifiers. This format is useful for dumping main part of Allele Registry database (allele
definitions and CA/PA identifiers).
Example
Request: reg.genome.network/allele/CA000559.txt
Response:
NC_000010.11:g.87957955C>T
CA559
Alleles Database
Alleles database consists of several files, each of them corresponds to single “table”. The most
important are the three following files:
•
genomic
•
protein
•
sequence
They contain all data stored by Allele Registry. If the Registry cannot find some of these files, it creates
new empty table (it allows to start Registry without database).
The database contains also additional “tables”, which work as indexes:
•
idCa
•
idPa
•
idClinVarAllele
•
idClinVarRCV
•
idClinVarVariant
•
idDbSnp
If at least one of these files is missing when Registry process is starting, the Registry tries to rebuild
missing index (or indexes) by performing full scan of “genomic” and “protein” tables. During this
procedure, identifiers of proper types are collected and missing indexes are built from scratch. The full
scan procedure may take long time for large databases.
Administrator’s API for managing
alleles and external identifiers
As “identifiers” we understand here all identifiers presented in the section “externalRecords” in Allele’s
document. It includes identifiers imported from large datasets like dbSNP, MyVariant.Info or gnomAD.
Import new identifiers
This is an extended version of the request used for bulk registration of new alleles that was described in
API specification (see “Bulk query of alleles with HGVS expressions or identifiers” and “Register new
alleles”). When the request is sent by an administrator, a payload may contain additional columns with
identifiers to register.
The content sent as payload is processed in the following way:
1. the system identify the variant by “Key” column (variant definition or CA/PA ID)
2. if the variant is not in the database, it is automatically registered (CA/PA ID is assigned)
3. all defined identifiers are added to the variant; if given identifier is already registered (with
exactly the same type and value), it is ignored
4. the request returns vector of Allele documents, each document corresponds to single line in the
payload
The payload must contain exactly one “Key” column. The only exception is allowed, when CA/PA ID
column is defined along with the other “Key” column – in this special case, variants from payloads are
recognized by the other “Key” column and registered with given CA/PA ID values. This special case is
very dangerous and should be used only in exceptional situation. The uniqueness of CA/PA ID is
not verified by the system, the administrator has to make sure that submitted variants and
CA/PA identifiers are unique.
Request
PUT /alleles
Parameters
•
file – contains non-empty list of columns names separated by plus characters (‘+’). This
expression defines the format of a payload. The expression must meet the following conditions:
◦ the same column name cannot appear twice in the expression, the only exception is ignored
column represented by empty string in the file parameter
◦ the expression must contain exactly one “Key” column, the only exception is CA/PA ID
column represented by “id”; it can be used together with other “Key” column (see special
case in the description above)
The table below summarize all supported columns names:
Column name
Key?
Required format in payload
hgvs
Yes
well-defined HGVS expression
id
Yes
CA ID or PA ID
MyVariantInfo_hg19.id
Yes
e.g. chr9:g.107620835G>A
MyVariantInfo_hg38.id
Yes
the same as above
ExAC.id
Yes
e.g. 5-112043382-A-G
gnomAD.id
Yes
the same as above
(empty string)
No
this column is ignored, useful for files with extra columns
dbSNP.rs
No
a number or an empty string if none
ClinVar.alleleId
No
a number or an empty string if none
ClinVar.variationId
No
a number or an empty string if none
ClinVar.preferredName
No
a string, must have already a “ClinVar.alleleId” column
defined if non-empty
ClinVar.RCV
No
list of numbers separated by comma characters (‘,’), must have
already a “ClinVar.variationId” column defined if non-empty
COSMIC.id
No
COSMIC id with suffix “/0” (obsolete) or “/1” (active), e.g.:
COSM2240643/1
COSM5424721/0
COSN19651925/1
or an empty string if none
externalSource.{sourceName}
No
see “External sources” in API specification
Payload
It must contain list of records separated by end-of-line character. Each record must consist of the same
number of fields (columns) separated by a TAB character. The number and types of columns must
correspond to definition given in the “file” parameter described above.
Response
A vector of corresponding Allele documents in JSON. You probably should use “fields” parameter to
normalize processing time, like “fields=none+@id” (see “Adjusting response format” in API
specification).
Delete all identifiers of given type
These request deletes all identifiers (whole entries in “externalRecords” section) originating from given
external system.
Request
DELETE /externalRecords/{name}
{name} must be one of the following: dbSNP, ClinVar
Response
Empty JSON object.
Delete alleles by CA/PA IDs
This requests expects payload with list of CA/PA IDs (one per line). Existing alleles with given CA/PA
identifiers are deleted, along with assigned to them external identifiers and links from external sources.
This request is not suppose to be used under normal circumstances! It is non-standard in two
ways:
•
according to main assumptions of Allele Registry, registered alleles along with their
CA/PA identifiers are not supposed to be deleted
•
HTTP DELETE requests are not supposed to have a payload (many proxy servers do not
support that), so this request should be sent only to localhost
Request
DELETE /alleles?file=id
Payload
Single column with CA/PA identifiers
Response
A vector of corresponding JSON Allele documents, but only with some basic data.
Administrator’s API for External
Sources
See “Allele Registry API specification” for description of External Sources. This sections contains only
requests available from administrator’s level.
Final links and their labels are generated from patterns set in an External Source object. Patterns can
use references to external source parameters, that are substituted with proper values during generation
of final textual content. Currently, the following parameters references can be used: {id}, {p1}, {p2},
{p3}. The first one corresponds to raw integer value of CAR allele id, while values of other three
parameters are set by the user along with link definitions. Every parameter holding integer value can be
zero-padded by append to the parameter’s name a character “_” (underscore) followed by a number.
Eg.: to get “standard” CA identifier the pattern “CA{id_6}” may be used.
Create new external source
Request
PUT /externalSource/{sourceName}
{sourceName} – a name of the external source, it is used in API. The name can contain only
alphanumeric characters and underscores (0-9, a-z, A-Z, _).
Parameters
•
guiName - user-friendly name for external source
•
params - defines number and types of external source parameters. It must contain from 0 to 3
characters, each character must be S (string) or I (integers). E.g. .: SI means that an external
source has 2 parameters (p1 and p2), where p1 is a string and p2 is an unsigned integer.
•
url - pattern for API url, it is used for generation of the value of “@id” field
•
guiUrl - pattern for GUI url, it is used for generation of the value of “guiUrl” field
•
guiLabel - pattern for user-friendly link label, it is used for generation of the value of
“guiLabel” field
Modify existing external source
Name of the external source, as well as, number and types of its parameters cannot be altered.
Request
PUT /externalSource/{sourceName}
{sourceName} – a name of the external source
Parameters:
Exactly one of the following parameter must be set:
• guiName - new “guiName” parameter value, see the request above
• url - new “url” parameter value, see the request above
• guiUrl - new “guiUrl” parameter value, see the request above
• guiLabel - new “guiLabel” parameter value, see the request above
Delete external source
It deletes an external source with whole content, including all links.
Request
DELETE /externalSource/{sourceName}
{sourceName} – a name of the external source
Assign user to an external source
Request
PUT /externalSource/{sourceName}/user/{login}
{sourceName} - name of an external source
{login} - name of Genboree user, it is not verified by the system
Remove user from an external source
Request
DELETE /externalSource/{sourceName}/user/{login}
{sourceName} - name of an external source
{login} - name of Genboree user, it is not verified by the system
Unpublished standard API requests
This section list all API requests available for all users but not published in API specification. Since
they are not published, we do not have to support them in future releases.
Query all genomic alleles
In connection with “txt” protocol described in the Introduction it can used to dump to a simple text file
list of all genomic alleles.
Request
GET /genomicAlleles
Parameters
•
(optional) skip – standard pagination parameter
•
(optional) limit – standard pagination parameter
Response
An array of Allele objects.
Query all protein alleles
In connection with “txt” protocol described in the Introduction it can used to dump to a simple text file
list of all protein alleles.
Request
GET /proteinAlleles
Parameters
•
(optional) skip – standard pagination parameter
•
(optional) limit – standard pagination parameter
Response
An array of Allele objects.
Return basic properties of given reference sequence
Request
GET /refseq/{RSid}/sequence
Response
Returned object is similar to standard Reference Sequence document, but contains also some additional
fields like:
•
CDS – region of transcript’s coding sequences
•
sequence – sequence, for transcript it contains all introns
•
spliced sequence – transcript’s sequence after splicing (without introns)
Match protein and transcript variants for gene mutation
This request returns all matching variants for notation gene+mutation. Both protein and transcript
variants are calculated. If transcript mutation is given, protein mutations are calculated directly from
matching transcript mutations. If protein mutation is given, corresponding transcript mutations are
searched across registered alleles.
Request
GET /matchAlleles
Parameters
•
gene – symbol of gene (e.g. TP53, GALE)
•
variant – mutation in HGVS notation without reference (e.g.: c.930C>G, p.Asn310Lys)
Response
Not trivial.
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