VisANT Web Service API Guide:

The VisANT web services can be accessed by the following URL:

http://server_name:server_port/vserver/DAI?command=command&parameter_list

This document provides a reference guide to help you get started.

Command: link

Summary:

return : "http://visant.bu.edu/ws/test/visant"+jnlpNo+".jnlp"

Parameters:

  • [required] location=location

Output:

return : "http://visant.bu.edu/ws/test/visant"+jnlpNo+".jnlp"

*need an example URL

*PENDING

Command: alias

Summary:

do name normalization

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src

Output:

return : A text of name normalization results

Example:

http://visant.bu.edu:8080/vserver/DAI?command=alias&orf=YMR047C&species=sce&src=YMR047C

Example output:

YMR047C src_11,2AIV PDB,Q02630 SP,855066 loc,NSP116 Common Name,NUP116 Common Name,S000004650 SGD ID,S28925 PIR ID,X68108 acc_gene,CAA48228 acc_protein,CAA88413 acc_protein,Q02630 acc_protein,NP_013762 acc_protein,Nup116p desc,S28925 acc_protein,YMR047C Common Name,4052 gi_gene,4053 gi_protein,695727 gi_protein,1346645 gi_protein,6323691 gi_protein,320799 gi_protein,YMR047C original,YMR047C ORF@@

Output format:

[the_original_alias_user_entered][tab]src_11[comma] [A list of comma separated alias_name/alias_type pairs, format: alias_name+tab+alias_type][comma] [the_original_alias_user_entered][tab]original[comma] [orf_id][tab]ORF@@

FINISHED

Command: unilink

Summary:

return interactions

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src
  • [optional] db=db
  • (optional source db. default:null. currently, only "fln"(Functional Linkage Network interaction DB) is supported.

Output:

return : A text of interaction results

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=unilink&orf=YMR047C&species=sce&src=YMR047C

Example output:

Output Example

Output format({} means optional):

[the_output_result_of_alias_command][comma_separated_interaction_list: orf_id_1*orf_id_2:method_id:direction:refs{:wwweight}]

FINISHED

Command: unilinkx

Summary:

alternative name of unilink command, but with XML output format

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src
  • [optional] db=db
  • (optional source db. default:null. currently, only "fln"(Functional Linkage Network interaction DB) is supported.

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=unilinkx&orf=YMR047C&species=sce&src=YMR047C

Example Output:

return : A gzipped PSI-MI 2.5 XML document of aliases and interaction results

Output Example & format description

FINISHED

Command: lookup

Summary:

Do name normalization first then return interactions

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src
  • [optional] db=db
  • (optional source db. default:null. currently, only "fln"(Functional Linkage Network interaction DB) is supported.

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=lookup&orf=YMR047C&species=sce&src=YMR047C

Output:

return : Text of aliases and interaction results, which is the combination of return results of both alias command and unilink command

Output Example

Output format:

[the_same_output_of_command_alias][the_same_output_of_command_unilink]

FINISHED

Command: lookupx

Summary:

Same as command lookup, except that return XML document instead of text as output

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src
  • [optional] db=db
  • (optional source db. default:null. currently, only "fln"(Functional Linkage Network interaction DB) is supported.

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=lookupx&orf=YMR047C&species=sce&src=YMR047C

Output:

return : A PSI-MI V2.5 XML document of aliases and interaction results

Output Example & format description

FINISHED

Command: get_alias_type

Summary:

Get all alias type supported by the search box

Parameters: NONE

Output:

A XML document of all alias type supported by the search box

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=get_alias_type

Output Example & format description

FINISHED

 Command: methods

Summary:

return methods

Parameters:NONE

URL Example:

http://visant.bu.edu:8080/vserver/DAI?command=methods

Output:

return : Text content of all methods list

Output Example

Output format:

A list of all methods, where each method consists of: [method_id]:[method_name]:[method_weight]:[method_type(E:Experimental,C:Computational)];

FINISHED

Command: cogx

Summary:

Find all COG records(orf_id, gene_id) for a given gene

Parameters:

  • [required] orf=orf
  • [required] species=species
  • [required] src=src

Example:

http://visant.bu.edu:8080/vserver/DAI?command=cogx&orf=MAK3&species=spo&src=MAK3

Output:

return : Gzipped XML document of COG results

Output Example(gunzipped) & format description

FINISHED

Command: time*

Summary:

A collection of time commands.

Commands list:

  • command=time_report:
    parameters: stuff
    Output: String message
  • command=time_svg:
    parameters: visml_data, label_on, zoom_dim, version, rmode
    Output: String message
  • command=time_method:
    parameters: method, species
    Output: String message

    URL Example: http://visant.bu.edu:8080/vserver/DAI?command=time_method&method=M0067&species=hsa

    Output: Text content of all methods list

    Output Example

    Output format:

    #genomewide #method=[method_id] #species=[species_id]@@\n[interaction_list, format: orf_id_1*orf_id_2:direction:refs]

    FINISHED

  • command=time_proxy:
    parameters: target, plus arbitrary number of parameter pairs
    Output: String message
  • command=time_image_jpg:
    parameters: An upload image file
    Output: save the file and return a String message
  • command=time_orthology:
    parameters: orthology_type, species
    Output: String message

Command: go*

Summary:

A collection of go commands.

Commands list:

FINISHED

FINISHED

  • command=go_get_go_ancester:
    Return all the ancester GO IDs, recursively, for a given GO ID list
    The root node of the GO tree (all) is included in the return result.
    parameters:
    required: go_ids: a '|' separated multiple GO ID list('GO:' could be omitted)

    Output: one line text of GO IDs, separated by '|'

    URL Example:
    http://visant.bu.edu:8080/vserver/DAI?command=go_get_go_ancester&go_ids=0022610|0005623|0033747

    Sample output:
    all|0016209|0008150|0003824|0005575|0003674|0016491|0016684|0004601

Command: get_orfid_list

Summary:

Get a list of all orf_ids under a given species

Parameters:

  • [required] species=species

Output:

A XML document of orf_id list

Example:

http://visant.bu.edu:8080/vserver/DAI?command=get_orfid_list&species=hsa

Output Example & format description