KDBIO/INESC-ID IST BSRG/IST

YEASTRACT Web Services

Resources

Resources

Table 1: Resources

Resource

URI(s)

Description

Protein

/protein/{protein}

Represents a protein.

Locus

/locus/{locus}

Represents a locus (ORF/gene).

Regulations

/regulations/{documented,potential,both}?tf={tf1}&tf={tf2}&…&orf={orf1}&orf={orf2}&…

  • Documented, potential or both types of regulations involving each of the transcription factors and all of the supplied genes.

  • If no transcription factors or genes are provided uses all the transcription factors or genes in the database.

  • This URI template corresponds to the Search TFs / Search Genes operations in the YEASTRACT web interface.

Regulation references

/references/regulation?tf={tf1}&tf={tf2}&...&orf={orf1}&orf={orf2}&...

Represents a list of references for regulation between transcription factors and an ORF/genes.

Consensus references

/references/consensus?tf={tf1}&tf={tf2}&...&tfbs={tfbs1}&tfbs={tfbs2}&...

Represents a list of references between transcription factors and transcription factor binding sites.

Notes


/protein/{protein}

Description

Retrieves the information about a protein.

Input

A protein name.

Output

Returns the following data for the given protein:

  • protein name
  • description
  • aminoacid sequence
  • transcription factor binding site(s)
  • documented regulations
  • potential regulations
Example

Sample requests using curl:

Methods

GET

request parameters
parameter value description

protein

string

A protein (transcription factor) name.

available response representations:

  • application/json


/locus/{orf}

Description

Retrieves the information about an ORF/gene.

Input

An ORF/gene name.

Output

Returns the available information for the locus.

Example

Sample request using curl:

Methods

GET

request parameters
parameter value description

orf

string

An ORF or a gene name.

available response representations:

  • application/json


/regulations/{search-type}?tf={tf1}&tf={tf2}...&orf={orf1}&orf={orf2}...

Description

Searches for regulations between the transcription factors (TFs) and genes.

For further documentation, please refer to YEASTRACT's web interface help on the following items:


Input

One or more TFs and/or one or more genes and the type of regulation to search for.

Output

Returns a list of regulations between the transcription factors and the given genes, according to the search type.

Example

Sample request using curl:

Methods

GET

request parameters
parameter value description

search-type

string

One of:

  • documented
  • potential
  • both

Searches documented, potential or both types of regulations.

If not provided defaults to documented.

tf

string

A transcription factor. Repeat the parameter to provide multiple transcription factors.

orf

string

An ORF orf a gene name. Repeat the parameter to provide multiple ORF/gene names.

available response representations:

  • application/json


/references/regulation?tf={tf1}&tf={tf2}...&orf={orf1}&orf={orf2}...

Description

Returns bibliographic references about a regulation between a set of transcription factors and a set of ORF/genes.

Input

Takes as input, optionally, a list of ORF/gene names and a list of transcription factors.

Output

A list of references for the documented regulation between the transcription factors and the ORF/genes.

Example

Sample request using curl:

Methods

GET

request parameters
parameter value description

tf

string

A transcription factor. Repeat the parameter to provide multiple transcription factors.

orf

string

An ORF/gene name. Repeat the parameter to provide multiple gene names.

available response representations:

  • application/json


/references/consensus?tf={tf1}&tf={tf2}...&tfbs={tfbs1}&tfbs={tfbs2}...

Description

Returns bibliographic references between transcription factors and transcription factor binding sites.

Input

Takes as input, optionally, a list of transcription factors and a list of transcription factor binding sites.

Output

A list of references for the associations between the transcription factors and the transcription factor binding sites.

Example

Sample request using curl:

Methods

GET

request parameters
parameter value description

tf

string

A transcription factor. Repeat the parameter to provide multiple transcription factors.

tfbs

string

A transcription factor binding site. Repeat the parameter to provide multiple transcription factor binding sites.

available response representations:

  • application/json