Protocol Documentation

Uses a Golang RE2-syntax regex to match the field contents.

Field value of integer strictly greater than this value.

Field value of integer strictly smaller than this value.

Used for nested message types, requires that the message type exists.

Human error specifies a user-customizable error that is visible to the user.

Field value of double strictly greater than this value. Note that this value can only take on a valid floating point value. Use together with float_epsilon if you need something more specific.

Field value of double strictly smaller than this value. Note that this value can only take on a valid floating point value. Use together with float_epsilon if you need something more specific.

Field value of double describing the epsilon within which any comparison should be considered to be true. For example, when using float_gt = 0.35, using a float_epsilon of 0.05 would mean that any value above 0.30 is acceptable. It can be thought of as a {float_value_condition} +- {float_epsilon}. If unset, no correction for floating point inaccuracies in comparisons will be attempted.

Floating-point value compared to which the field content should be greater or equal.

Floating-point value compared to which the field content should be smaller or equal.

Used for string fields, requires the string to be not empty (i.e different from "").

Repeated field with at least this number of elements.

Repeated field with at most this number of elements.

Field value of length greater than this value.

Field value of length smaller than this value.

Field value of length strictly equal to this value.

Requires that the value is in the enum.

Ensures that a string value is in UUID format. uuid_ver specifies the valid UUID versions. Valid values are: 0-5. If uuid_ver is 0 all UUID versions are accepted.

Require that one of the oneof fields is set.

name of the sequence file

ncbi taxonid of the organism

name of the database

human readable description of the database

Type of sequence, nucleotide or protein

sequence needed for database, provided in chunks

ncbi taxonid of the organism

name of the database

human readable description of the database

Type of sequence, nucleotide or protein

name of the file

content of the file, expected to be streamed in chunk

Status gives the status after file upload

message send by the server after file upload

unique identifier for the annotation

unique identifier of a group

unique identifier for the annotation

list of unique identifiers

tag identifier

human readable name

ontology to which this tag belong

status for active or retired tag

unique identifier for the annotation

flag to indicate whether the entry will be wiped or turned obsolete(soft delete)

An identifiable tagname for the annotation, primarily a structured tag, generally an ontology term.

unique identifier of a biological entity that is being annotated

Name of ontology in which the tag name is taken

Ordering of annotation when an entry has multiple annotations with identical tag from the same ontology. By default, rank 0 is assumed.

Status for active or retired annotation. Active annotation is chosen by default.

unique identifier of a group

A unique pointer to the next set of result in the list

Maximum number of records that can be fetch per request

The `filter` field restricts the data return by the collection. To use it, supply one or multiple allowed fields to filter followed by a filter expression. It uses the following syntax... field_name operator expression The following fields of `AnnotationAttributes` definition are allowed to be used for filtering * entry_id - The entry that is being annotated (string) * created_by - Email id of the user (string) * tag - Tag name, a term from an ontology (string). * ontology - Ontology that provides the tag names (string). * rank - Ordering of annotation (number). operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded for http request. Operators for strings =~ Contains substring !~ Not contains substring === Equals !== Not equals Operators for numbers == Equals != Not equals > Greater than < Less than =< Less than equal to >= Greater than equal to expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded for http request. filter: "created_by==caboose@abc.com" filter: "entry_id==DDB_G4839483" filter: "tag==growth" Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR. filter: "tag~cytoskeletion;entry_id==DDB_G4839783;ontology==cellular" filter: "tag~membrane;entry_id==DDB_G4839783;ontology==cellular;rank=0"

A unique pointer to the next set of result in the list

Maximum number of records that can be fetch per request

The `filter` field restricts the data returned by the collection. It accepts one or more filtering conditions using the syntax: field_name operator expression Available fields for filtering from `AnnotationAttributes`: * entry_id - Identifier of the annotated entry (string) * value - Annotation text content (string) * created_by - Email of the creator (string) * tag - Ontology term used as tag (string) * ontology - Source ontology name (string) * version - Version number (number) * rank - Ordering of annotation (number) * is_obsolete - Status of annotation (boolean) String operators: * =~ Contains substring * !~ Does not contain substring * === Equals exactly * !== Not equals Numeric operators: * == Equals * != Not equals * > Greater than * < Less than * =< Less than or equal to * >= Greater than or equal to Boolean operators: * == Equals * != Not equals Examples: filter: "created_by===caboose@abc.com" filter: "entry_id===DDB_G4839483" filter: "value=~actin" filter: "tag===GO:0005634" filter: "ontology===cellular_component" filter: "version>3" filter: "rank==0" filter: "is_obsolete==false" filter: "value!~pseudogene" filter: "created_by!==anonymous@dictybase.org" Combine filters with boolean operators: * OR: represented by comma (,) * AND: represented by semicolon (;) * AND takes precedence over OR Example of combined filters: filter: "value=~cytoskeleton;tag===cell membrane;ontology===cellular" filter: "entry_id===DDB_G0285418;is_obsolete==false" filter: "created_by===curator@dictybase.org;version>2;rank==0" filter: "tag===GO:0005634,tag===GO:0005737" (entries with nuclear OR cytoplasmic localization) filter: "ontology===molecular_function;value=~transport" (transport-related functions) Note: URL-reserved characters must be properly encoded in HTTP requests.

A unique pointer to the next set of result in the collection. Set the cursor value parameter to the value of next_cursor to retrieve the next set of collection using the same method

Maximum number of records that can be fetch per request

resource name, by default should be annotation

annotation in plain text format

serialized text content in a format recognized by frontend rich text editor

Unique identifier(generally email) of the user who created the annotation

An identifiable tagname for the annotation, primarily a structured tag, generally an ontology term.

unique identifier of a biological entity that is being annotated

Name of ontology from which the tag name is taken

Ordering of annotation when an entry has multiple annotations with identical tag from the same ontology. By default, rank 0 is used.

human readable name

ontology to which this tag belong

status for active or retired tag

resource name, by default should be annotation

unique identifier for the annotation

annotation in plain text format

serialized text content in a format recognized by frontend rich text editor

Unique identifier(generally email) of the user who created the annotation Timestamp for creation

An identifiable tagname for the annotation, primarily a structured tag, generally an ontology term.

version refers to the current version no

unique identifier of a biological entity that is being annotated

Name of ontology in which the tag name is taken

Ordering of annotation when an entry has multiple annotations with identical tag from the same ontology.

Status for active or retired annotation

resource name, by default should be annotation

unique identifier for the annotation

unique identifier for the annotation group

Timestamp for creation an update

resource name, by default should be annotation

unique identifier for the annotation

resource name, by default it should be annotation group

resource name, by default should be annotation

unique identifier for the annotation

annotation in plain text format

serialized text content in a format recognized by frontend rich text editor

Unique identifier(generally email) of the user who created the annotation

The resource name.

Unique id.

A http link. It points to the resource itself.

A http link. It points to a related resource.

Total number of entries, regardless of pages.

Total number of pages.

Number of entries per page.

Current page number.

A http link to the resource itself.

A http link to the next page of data.

A http link to the previous page of data.

A http link to the last page of data.

A http link to the first page of data.

An unique identifier, for example: "/users/34"

exist or non-existant

Email id "/users/newman@seinfeld.org"

include query parameter to retrieve any particular or particular combination of relationships. Multiple include values are delimited by comma(,). For example, /{resource_name}/13?include=baz /{resource_name}/13?include=baz,bot

fields query parameter to retrieve any particular or any particular combination of attributes. Multiple fields values are delimited by comma(,). For example, /{resource_name}/29?fields=foo /{resource_name}/?fields=foo,bar

An unique identifier, for example: "/users/34"

include query parameter to retrieve any particular or particular combination of relationships. Multiple include values are delimited by comma(,). For example, /{resource_name}/13?include=baz /{resource_name}/13?include=baz,bot

fields query parameter to retrieve any particular or any particular combination of attributes. Multiple fields values are delimited by comma(,). For example /{resource_name}/29?fields=foo /{resource_name}/?fields=foo,bar

An unique identifier, for example: "/users/34"

fields query parameter to retrieve any particular or any particular combination of attributes. Multiple fields values are delimited by comma(,). For example /{resource_name}/29?fields=foo /{resource_name}/?fields=foo,bar

An unique identifier

An unique identifier

include query parameter to retrieve any particular or particular combination of relationships. Multiple include values are delimited by comma(,). For example, /{resource_name}/13?include=baz /{resource_name}/13?include=baz,bot

fields query parameter to retrieve any particular or any particular combination of attributes. Multiple fields values are delimited by comma(,). For example /{resource_name}/29?fields=foo /{resource_name}/?fields=foo,bar

The page number to fetch

Number of records per page

The `filter` query parameter restricts the data return by the collection. To use it, supply an attribute to filter, followed by a filter expression. It uses the following syntax... attribute operator expression attribute - Any one of the valid attribute of the resource. operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded. == Equals (URL encoding is %3D%3D) != Not equals =@ Contains substring !@ Not contains substring expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded. For example, the following filter returns all users with last name `Gag`. /users?filter=last_name%3D%3Dgag Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR.

An unique identifier, for example: "/users/45/roles" or "/users/45/relationships/roles"

include query parameter to retrieve any particular or particular combination of relationships. Multiple include values are delimited by comma(,). For example, /{resource_name}/13?include=baz /{resource_name}/13?include=baz,bot

fields query parameter to retrieve any particular or any particular combination of attributes. Multiple fields values are delimited by comma(,). For example /{resource_name}/29?fields=foo /{resource_name}/?fields=foo,bar

The `filter` query parameter restricts the data return by the collection. To use it, supply an attribute to filter, followed by a filter expression. It uses the following syntax... attribute operator expression attribute - Any one of the valid attribute of the resource. operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded. == Equals (URL encoding is %3D%3D) != Not equals =@ Contains substring !@ Not contains substring expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded. For example, the following filter returns all users with last name `Gag`. /users?filter=last_name%3D%3Dgag Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR.

resource name

An unique identifier provided by the third party. Generally it's an email id, however it could be something else specifically provided by an provider.

Name of the provider, for example, orcid, google, facebook etc.

The id of the user to which this identity is connected. This id could be used to fetch a complete user response from the user service

Timestamp for creation and update

The resource name

Unique id

An unique identifier provided by the third party. Generally it's an email id, however it could be something else specifically provided by an provider.

Name of the provider, for example, orcid, google, facebook etc.

An unique identifier provided by the third party. Generally it's an email id, however it could be something else specifically provided by an provider.

Name of the provider, for example, orcid, google, facebook etc.

The id of the user to which this identity is connected. This id could be used to fetch a complete user response from the user service

Http links with role resource.

A role [resource identifier object](http://jsonapi.org/format/#document-resource-identifier-objects).

A role [resource identifier object](http://jsonapi.org/format/#document-resource-identifier-objects).

Kind of permission, for example read, write, admin etc.

Brief description of the type of permission.

Timestamp for creation and update

Resource(object) on which this permission is granted

The resource name.

Unique id.

Timestamp for creation and update

Unique id, required

An optional mask specifying which fields to update. Presence of this field allow partial updates.

Unique id, required

An optional mask specifying which fields to update. Presence of this field allow partial updates.

Unique id, required

An optional mask specifying which fields to update. Presence of this field allow partial updates.

First name.

Last name.

Email.

Organization in which the user belong.

Group in which the user belong.

Address.

More address.

City.

State.

Zipcode.

Country.

Phone no.

Current status of user.

Timestamp for creation and update

The resource name.

Unique id.

JSON Web Token (JWT)

Refresh token

Identity of user

User API data

Client ID received during application registration from every provider

Scope of the application

An unguessable random string. It is used to protect against cross-site request forgery attacks. It is passed to the provider during first login.

The URL in the application where users will be sent after authorization, generally provided during the registration of the application.

The code that is received as response from the first login

Third party oAuth provider

Refresh token (unique ID)

Refresh token

JSON Web Token (JWT)

Refresh token (unique ID)

JSON Web Token (JWT)

Refresh token (unique ID)

page name

page slug. Look here https://en.wikipedia.org/wiki/Semantic_URL#Slug to know about slug

email id of the user who created the content

email id of the user who updated the content

Timestamp for creation and update

serialized page content(for example serialized draft js object)

namespace for the page

unique identifier for the annotation

The resource name

Unique id

Unique id to identify content

Url slug Look here https://en.wikipedia.org/wiki/Semantic_URL#Slug to know about slug The slug name should be unique

email id of the user who is updating this content

serialized page content(for example serialized draft js object)

A unique pointer to the next set of result in the list

Maximum number of records that can be fetch per request

The `filter` field restricts the data return by the collection. To use it, supply one or multiple allowed fields to filter followed by a filter expression. It uses the following syntax... field_name operator expression The following fields of `ContentAttributes` definition are allowed to be used for filtering * name - page name (string). * slug - page slug (string). * namespace - page namespace (string). * created_by - Email id of the user (string) operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded for http request. Operators for strings =~ Contains substring !~ Not contains substring === Equals !== Not equals expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded for http request. filter: "name===annotation" filter: "slug=~frontpage" filter: "namespace===dsc" Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR. filter: "name~gallery;namespace===stockcenter;slug===intro"

A unique pointer to the next set of result in the collection. Set the cursor value parameter to the value of next_cursor to retrieve the next set of collection using the same method

Maximum number of records that can be fetch per request

page name

email of the user who is creating this content

page content, expected to be serialized `JSON` string.

namespace for the page, it is prepended to the name to generate an unique slug.

page slug. Look here https://en.wikipedia.org/wiki/Semantic_URL#Slug to know about slug

resource name

An optional mask specifying which fields to update. Presence of this field allow partial updates.

resource name

unique id

ID of feature annotation to modify

Tag to be added

ID of feature annotation to modify

Tags to be added

DOI to search for (e.g. "10.1234/abcd.1234")

Identifier of the linked database

a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant

Source database

Type of this dblink, for example 'protein'

URL that is associated with this link

A short name that is a possible alternative to the database name which could be used for display.

Identifier

Source database

unique identifier for the feature annotation

flag to indicate whether the entry will be wiped or turned obsolete(soft delete)

unique identifier for the feature annotation

email id of the user who created the content

email id of the user who updated the content

Timestamp for creation and update

Toggle the obsolete status

Deprecated.

Short human readable textual name

Alternate list of names

List of publications(doi identifiers)

List of pubmed id

Deprecated.

Cross references to other databases

Bucket of key value pair data

Collection of feature annotations

unique identifier for the feature annotation

Deprecated. DEPRECATED: Use update_attributes field instead. This field is maintained for backward compatibility and will be removed in a future version.

email id of the user who updated the content

Toggle the obsolete status

New field for partial updates with all optional fields. When both attributes and update_attributes are provided, update_attributes takes precedence.

Short human readable textual name

Alternate list of names

List of publications(doi identifiers)

List of pubmed id

Cross references to other databases

Bucket of key value pair data

Feature name to search for

email id of the user who created the content

Timestamp for creation and update

Toggle the obsolete status

Deprecated.

unique identifier for the feature annotation

PubMed ID to search for

Deprecated. ID of feature annotation to modify

Deprecated. Tag to remove

ID of feature annotation to modify

Tag name to remove

Tag value to remove

ID of feature annotation to modify

Complete set of tags to replace all existing tags

email id of the user who created the tag

email id of the user who updated the tag

Timestamp for creation and update

email id of the user who created the tag

Timestamp for creation

Deprecated.

Deprecated.

Deprecated. email id of the user who created the tag

Deprecated.

Deprecated. ID of feature annotation to modify

Deprecated. Updated tag values

unique identifier for the organism

email id of the user who created the content

email id of the user who created the content

email id of the user who updated the content

Unique identifier for the organism

Abbreviated name of the organism

Common name of the organism

Genus name

Species name

Collection of organisms

unique identifier for the organism

unique identifier for the organism

email id of the user who updated the content

Resource name, by default should be order

Time order was created

Time order was updated

Person who is ordering (logged in user)

List of items in the order, in this case it will be mostly biological stocks such as plasmids and strains

A unique pointer to the next set of result in the list

Maximum number of records that can be fetch per request

The `filter` field restricts the data return by the collection. To use it, supply one or multiple allowed fields to filter followed by a filter expression. It uses the following syntax... field_name operator expression The following fields of `OrderAttributes` definition are allowed to be used for filtering * item - Items that are part of order (string). * courier - The courier used for delivery (string) * payment - Type of payment being used (string) * status - The status of the order (string) * created_at - Date the items are ordered (number), can be in the following formats: YYYY-MM-DD, YYYY-MM, YYYY field_name - Any one of the allowed field_name of the `OrderAttributes` definition. operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded for http request. Operators for strings =~ Contains substring !~ Not contains substring === Equals !== Not equals Operators for number == Equals > Greater than < Less than <= Less than equal to >= Greater than equal to Operators for dates $== Equals $> Greater than $< Less than $<= Less than equal to $>= Greater than equal to expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded for http request. filter: "status===Shipped" filter: "courier===FedEx" Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR. filter: "courier===FedEx;payment===Credit" filter: "created_at$>=20181201" The sort field allow to sort the data return by the collection based on fields of `OrderAttributes. To use it, supply a comma separated one or more allowed field from the definition of `OrderAttributes`.

A unique pointer to the next set of result in the collection. Set the cursor value parameter to the value of next_cursor to retrieve the next set of collection using the same method

Maximum number of records that can be fetch per request

Total number of records in the collection.

Resource name, by default should be order

Name of courier for delivery

Account identification used for courier service

Any comments about the order

Type of payment being used

Order number for purchase

Status of order

Person (user) who is receiving the stocks in mail

Person (user) who is paying for the stocks

Person who is ordering (logged in user)

List of items in the order, in this case it will be mostly biological stocks such as plasmids and strains

Resource name, by default should be order

Unique identifier for the order

Timestamp for creation

Timestamp for update

Name of courier for delivery

Account identification used for courier service

Any comments about the order

Type of payment being used

Order number for purchase

Status of order

Person (user) who is receiving the stocks in mail

Person (user) who is paying for the stocks

Person who is ordering (logged in user)

List of items in the order, in this case it will be mostly biological stocks such as plasmids and strains

Resource name, by default should be order

Unique identifier for the order

Unique identifier for the order

Resource name, by default should be order

Unique identifier for the order

Name of courier for delivery

Account identification used for courier service

Any comments about the order

Type of payment being used

Order number for purchase

Status of order

List of items in the order, in this case it will be mostly biological stocks such as plasmids and strains

Last name of the author

First name of the author

Any initials of the author

Ranking of the author

A unique pointer to the next set of result in the list

Maximum number of records that can be fetch per request

The `filter` field restricts the data return by the collection. To use it, supply one or multiple allowed fields to filter followed by a filter expression. It uses the following syntax... field_name operator expression The following fields of `PublicationAttributes` definition are allowed to be used for filtering * journal - Journal where the publication was published (string) * year - Year publication was published (string) * pub_date - Date of publication (string) * pub_type - Type of publication (string) * source - Source of the publication (string) * issue - Issue of the publication (string) * status - Status of the publication (string) * author - Authors of the publication (string) field_name - Any one of the allowed field_name of the `PublicationAttributes` definition. operator - Defines the type of filter match to use. It could be any of the following four and all of them should be URL-encoded for http request. Operators for strings =~ Contains substring !~ Not contains substring === Equals !== Not equals Operators for number == Equals > Greater than < Less than =< Less than equal to >= Greater than equal to expression - The value that will be included or excluded from the result. URL-reserved characters must be URL-encoded for http request. filter: "pub_type===journal_article" filter: "source===pubmed" Filter can be combined using OR or AND boolean logic. * The OR is represented using a comma(,). * The AND is represented using a semi-colon(;). * AND and OR operators can be combined and AND takes precedence over OR. filter: "year==2008;journal===Genesis" Can also accept multiple authors. filter: "author===Vandelay;author===VanNostrand" The sort field allow to sort the data return by the collection based on fields of `PublicationAttributes. To use it, supply a comma separated one or more allowed field from the definition of `PublicationAttributes`.

A unique pointer to the next set of result in the collection. Set the cursor value parameter to the value of next_cursor to retrieve the next set of collection using the same method

Maximum number of records that can be fetch per request

Total number of records in the collection.

Resource name, by default should be publication

Resource name, by default should be publication

Unique identifier for the publication

Digital object identifier for publication

Title of publication

Abstract of publication

Journal where the publication was published

Date publication was published

Volume of the publication

Pages containing the publication

International Standard Serial Number of publication

Type of publication (i.e. "journal_article")

Source of the publication (i.e. "pubmed")

Issue of the publication

Status of the publication

List of authors of the publication

Resource name, by default should be publication

Unique identifier for the publication

Unique identifier for the publication

Resource name, by default should be publication

Unique identifier for the publication

Date of publication

Volume of the publication

Pages containing the publication

Type of publication (i.e. "journal_article")

Source of the publication (i.e. "pubmed")

Status of the publication

List of authors of the publication

Resource name

Existing plasmid ID

Timestamp for creation

Timestamp for update

User who created stock entry

User who updated stock entry

Summary of the stock

Editable version of the stock summary (Slate JSON format)

List of associated genes

List of database cross references

Depositor of the stock

List of related publications

Image map for the plasmid

Sequence for the plasmid

Unambiguous name for the plasmid

dictybase specific plasmid property that will map to dicty_plasmid_keyword ontology