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
Command: alias
Command: unilink
Command: lookup
Command: get_alias_type
Command: methods
Command: kgml
Command: cog
Command: cogx
Command: time*
Command: go*
Command: get_orfid_list

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

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

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

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

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_method_xml:
parameters: method, species
Output: String message
command=time_tab | time_visML:
parameters: tab_data
Output: PENDING
URL Example: http://visant.bu.edu:8080/vserver/DAI?command=time_tab&tab_data=???

Output Example

PENDING

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:

command=go_annotation:

required parameters: orf, species

optional parameters:
go_mode
(1) none(not specified): default to return all go annotations
(2)"informative1": find out all "informative" GO annotations which meet the following ONE condition:
(i) at least [cutoff_value] genes are annotated with the term
(3)"informative2": find out all "informative" GO annotations which meet the following TWO conditions:
(i) at least [cutoff_value] genes are annotated with the term
(ii) none of its descendant terms are used to annotate over [cutoff_value] genes
(4)"sel_only": requires an additional parameter: go_id_list
Format: "|" separated GO ID list

return a subset of the given GO ID list with those GO IDs not associated with
the given orf_id filtered out. Here "associated" means:
The orf_id is annotated with that GO ID or an offspring GO ID of that GO ID

cutoff: applies to the 2 informative modes only
An integer for the above informative GO annotation modes.
Typical value for human species("hsa") is: 175
If not specified, system default value will apply.

branch_go_id: applies to go_mode (1,2,3) only
If specified, it means return a subset GO IDs of the results only,
which each of those is an offspring of the given branch_go_id

Output: XML document of go annotation

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation&orf=TP53&species=hsa
Output Example & format description

URL Example("go_mode:informative1"):
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation&orf=TP53&species=hsa&go_mode=informative1&cutoff=175
Output Example & format description

URL Example("go_mode:informative2"):
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation&orf=TP53&species=hsa&go_mode=informative2&cutoff=175
Output Example & format description

URL Example("go_mode:sel_only"):
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation&species=hsa&orf=ECGF1&go_mode=sel_only&go_id_list=GO:0034657|GO:0044424|GO:0000002|GO:0001568
Output Example & format description

command=go_informative:

required parameters:
species
go_mode: "informative1" or "informative2"
go_ids: a "|" separated GO id list

optional parameters:
cutoff:
An integer for the informative GO annotation modes.
Typical value for human species("hsa") is: 175
If not specified, system default value will apply.
alternative_xml_format: optional boolean value.
If true, means out in an alternative XML format which is easier to parse

Output: XML document of go annotation

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_informative&go_mode=informative1&species=hsa&go_ids=GO:0000739|GO:0003682|GO:0003700|GO:0000060|GO:0001701|GO:0001836|GO:0005626|GO:0005634|GO:0005654|GO:0005657
Output Example & format description

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_informative&go_mode=informative2&species=hsa&go_ids=GO:0000739|GO:0003682|GO:0003700|GO:0000060|GO:0001701|GO:0001836|GO:0005626|GO:0005634|GO:0005654|GO:0005657
Output Example & format description

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_informative&go_mode=informative2&alternative_xml_format=true&species=hsa&go_ids=GO:0000739|GO:0003682|GO:0003700|GO:0000060|GO:0001701|GO:0001836|GO:0005626|GO:0005634|GO:0005654|GO:0005657
Output Example & format description

command=go_term_ann:
parameters: acc(GO ID)
Output: String (term name)
URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_term_ann&acc=GO:0030154

Output: the GO name associated with the GO ID

Output Example:
cell differentiation

FINISHED

command=go_get_term_node:
required parameters: go_id e.g.: GO:0008150
optional parameters:
- depth: integer, how many sub-levels returned, default:4, minimum:1, maximum:7]
- get_gene_list: boolean, value: [true|false]. default: false
if true: means return all the genes annotated under this Term node also (node only, no recursive).
- species: string, example: 'hsa'. valid only then get_gene_list=ture. if specified, means return results for the given species only

Output: Gzipped XML document of the GO term tree

URL Example (get_gene_list=false):
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_node&go_id=0048308&depth=2
Output Example & format description
URL Example (get_gene_list=true):
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_node&go_id=0048308&depth=2&get_gene_list=true
Output Example & format description
URL Example (get_gene_list=true, species=sce):
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_node&go_id=0048308&depth=2&get_gene_list=true&species=sce
Output Example & format description

command=go_get_term_gene_list:
parameters:
go_id:string
node_only: boolean, optional, default: false.
If true: return the orf_id list which under the given node ONLY.
If false: return the orf_id list including not only those under this node,
but also all orf_ids under all offspring nodes of the given node(recursively).
- species: string, optional. example: 'hsa'. if specified, means return results for the given species only

Output: Gzipped XML document of all the orf_ids under the given GO term ID

URL Example:(node_only=false)
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_gene_list&go_id=0048308
Output Example & format description
URL Example:(node_only=false, species=spo)
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_gene_list&go_id=0048308&species=spo
Output Example & format description
URL Example:(node_only=true)
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_gene_list&go_id=0048308&node_only=true
Output Example & format description

command=go_get_term_gene_list_batch:
parameters:
go_ids: required. '|' separated GO ID list
species: required. example: 'hsa'.

Output: Gzipped XML document of all the orf_ids recursively under each of the given GO term ID

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_gene_list_batch&species=hsa&go_ids=0001832|0032868
Output Example & format description

command=go_annotation_route:
parameters:
required: go_id
Format: "|" separated GO ID list (prefix of "GO:" can be omitted), maximum of 100
If given more than 100 GO IDs, will report error.
Error handling: If any one of the given GO IDs doesn't exist, will return "not found" error message.

Output: Gzipped XML document of all the possible routes from the given GO ID to the root of the GO tree
The first GO ID of each route is the inquiried GO ID.

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation_route&go_id=GO:0034657|GO:0044424
Output Example & format description

FINISHED

command=go_annotation_search:
parameters:
required: keywords
Format: "|" separated keyword list, example: "metabolic|process"
can also be mixed with multiple GO ID list(each must start with uppercase 'GO:')
Example: "metabolic|process|GO:0008150"

Output: Gzipped XML document of all the possible routes from the matched GO ID to the root of the GO tree
Multiple GO ID results possible and supported.

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation_search&keywords=metabolic|process
Output Example & format description

command=go_get_term:
Return all the GO ids recursively associated with all genes of the given species.
Here, recursively means: Trace back to the whole term tree to find out all the ancester GO IDs
for each of the GO IDs found.
parameters:
required: species
optional:
branch_go_id: "|" separated GO ID list, example: "GO:0008150|GO:0005575"
means return all those GO ids which are under the branch of one of the given branch_go_ids
if not specified, means return all.

Output: Gzipped XML document of all the GO ids

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term&species=hsa&branch_go_id=GO:0008150|GO:0005575
Output Example & format description

command=go_annotation_list_only:
parameters:
required: species
required: orf
required: go_id
Format: "|" separated GO ID list (prefix of "GO:" can be omitted)

Output: XML document of GO ID list.
which is a subset of the given GO ID list with those GO IDs not associated with
the given orf_id filtered out. Here "associated" means: The orf_id has a GO annotation ID or an offspring of that GO ID
URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_annotation_list_only&species=hsa&orf=ECGF1&go_id=GO:0034657|GO:0044424|GO:0000002|GO:0001568
Output Example & format description

--depreciated. This command has been replaced by another command:
go_annotation with parameter: go_mode=sel_only&go_id_list=[GO_ID_list]

command=get_orfid_go_list:
parameters:
required: species
Format: "|" separated GO ID list (prefix of "GO:" can be omitted)

Output: Gzipped XML document of all the orf_ids of the given species,
together with GO IDs directly (not recursively) annotated to each orf_id.

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_get_orfid_go_list&species=hsa
Output Example & format description

command=go_get_term_similarity:
parameters:
required: go_id1
required: go_id2

Output: one line text of the GO term similarity score value(double precision).

URL Example:
http://visant.bu.edu:8080/vserver/DAI?command=go_get_term_similarity&go_id1=0000001&go_id2=0000002
Sample output:0.487358795051103

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