A command-line client written in Perl is available for download (it may require a few Perl modules to be installed if you don't have a recent Perl distribution); its command line syntax is available in the general HitKeeper documentation. - This page describes the server REST interface that is used by the client and that is meant to be called directly.

The different operation are called by specifying the action=... parameter, as in the following example

http://myhits.isb-sib.ch/cgi-bin/hk/restserv?action=seq_list

or to be even more REST styled

http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_list

The supported action parameters are the following: connect, disconnect, seq_list, mot_list, cla_list, hit_list, hat_list, hot_list, seq_info, mot_info, cla_info, seq_hk, mot_hk, cla_hk, hit_info, hat_info, hot_info, seq_parse_name, mot_parse_name, cla_parse_name, seq_query, mot_query, cla_query, hit_query, hat_query, hot_query, mom_query, seq_fetch_name, mot_fetch_name, cla_fetch_name, seq_fetch_desc, mot_fetch_desc, cla_fetch_desc, seq_fetch_entry, mot_fetch_entry, cla_fetch_entry, seq_fetch_prop, mot_fetch_prop, cla_fetch_prop, seq_fetch_fasta, mot_fetch_fasta, seq_fetch_nr, mot_fetch_nr, seq_dump_name, mot_dump_name, cla_dump_name, seq_dump_desc, mot_dump_desc, cla_dump_desc, seq_dump_entry, mot_dump_entry, cla_dump_entry, seq_dump_prop, mot_dump_prop, cla_dump_prop, seq_dump_fasta, mot_dump_fasta, seq_dump_nr, mot_dump_nr, hit_fetch_simple, hat_fetch_simple, hot_fetch_simple, query_list, query_info, query_stat, query_reset, default_list, default_set, sticker, . They are documented below with the additional parameters that can be supplied.

The service is stateful:

  • The connect action starts a new session and returns a session identifier that can be passed in subsequent calls using session_id=.... If your client accepts cookies, the session identifier does not need to be passed explicitly (i.e. a cookie is used for that purpose).
  • If you only intend to connect as a public guest (an anonymous connection), connect without supplying any username and password - or just skip the connection step if your client accepts cookies anyway (a session is created by default).
  • The disconnect action actually remove the cookie and terminate the session. The query_reset action can be used to refresh the query stack without removing the cookie.

Many parameters accept a list of values as argument:

  • Use commas to separate multiple items like for example in seq_name=THIO_RAT,THIO_MOUSE,THIO_HUMAN

For many actions, there exist build-in limits with the primary purpose of protecting the server and the client from being overflowed with data. The -lim=... and -tim=... parameters permit to alter these limits:

  • The -tim=... parameter allows to specify a timeout in second which is applied on individual SQL request (on the server back end). By default, the timeout is set to 10 s, but it can be increased up to 180 s. Note that that the overall time spent by an HTTP request can exceed the timeout value, when for example several individual SQL requests are executed. Note, too, that a request may timeout because it is intrinsically too long, or simply because the server is overloaded
  • The -lim=.... parameter allows to specify the maximal number of "rows" an individual SQL request is allowed to return (on the server back end). By default, this parameter is set to 1000, but it can be increased up to 300000. A warning is always issued when a result is possibly truncated. By using a value equal or below 1000 "rows", one can expect a faster response from the server.
  • The -format=xml option allows to request for an XML-fomatted output (if you like it)

Beware that the '+' character in an URL is translated into a space. Use '%2B' if you really want to mean 'plus'.


action=connect

Return the session_id string to be used in other methods. Do not set username and password to login anonymously.

username=...The name of a user with an account. [optional]
password=...The corresponding password. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/connect


action=disconnect

Terminate the current session.

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/disconnect


action=seq_list

Summary information about all sequence databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_type=...A non-empty list of sequence types. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_list


action=mot_list

Summary information about all motif databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_type=...A non-empty list of motif types. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_list


action=cla_list

Summary information about all classification databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_type=...A non-empty list of classification types. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_list


action=hit_list

Summary information about all computed hit lists (sequence vs motif)

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_type=...A non-empty list of sequence types. [optional]
mot_type=...A non-empty list of motif types. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hit_list


action=hat_list

Summary information about all 'hat' lists (sequence vs classification)

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hat_list


action=hot_list

Summary information about all 'hot' lists (motif vs classification)

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hot_list


action=seq_info

Miscellaneous information about sequence databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_info?seq_source=sw


action=mot_info

Miscellaneous information about motif databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_info?mot_source=pat,ft


action=cla_info

Miscellaneous information about classification databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_info?cla_source=taxid


action=seq_hk

HitKeeper information about sequence databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_hk?seq_source=sw


action=mot_hk

HitKeeper information about motif databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_hk?mot_source=pat,ft


action=cla_hk

HitKeeper information about classification databases.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_hk?cla_source=taxid


action=hit_info

Miscellaneous information about hit lists (sequence vs motif).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
mot_source=...A non-empty list of motif database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hit_info?seq_source=sw&mot_source=pat,ft


action=hat_info

Miscellaneous information about 'hat' lists (sequence vs classification).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
cla_source=...A non-empty list of classification database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hat_info?seq_source=sw&cla_source=taxid


action=hot_info

Miscellaneous information about 'hat' lists (motif vs classification).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
cla_source=...A non-empty list of classification database names. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hot_info?mot_source=pat,ft&cla_source=taxid


action=seq_parse_name

Internal routine not (yet) really useful.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-ref=...A query identifier [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_parse_name?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_parse_name

Internal routine no (yet) really useful

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-ref=...A query identifier [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_parse_name?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_parse_name

Internal routine not (yet) really useful.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-ref=...A query identifier [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_parse_name?cla_name=taxid:9606


action=seq_query

For querying the sequences. Refer to HELP(seq_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [optional]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_seq_name=...A list of sequence entry names to be included in the results (logical AND with the previous constraint). [optional]
not_seq_name=...A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
desc_text=...A list of words to search for. [optional]
min_score=...A positive real number. [optional]
prop_key=...Limit the search to the sequence with the given property key(s). [optional]
prop_value=...Limit the search to entries with the supplied property value(s). The exhaustive list of all entries matching the criteria is returned. This is a major distinction from the built-in synonymy mechanism that returns at most one sequence. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_query?seq_source=sw&seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_query

For querying the motifs. Refer to HELP(mom_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [optional]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_mot_name=...A list of motif entry names to be included in the results (logical AND with the previous constraint). [optional]
not_mot_name=...A list of motif entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
desc_text=...A list of words to search for. [optional]
min_score=...A positive real number. [optional]
prop_key=...Limit the search to the sequence with the given property key(s). [optional]
prop_value=...Limit the search to entries with the supplied property value(s). The exhaustive list of all entries matching the criteria is returned. This is a major distinction from the built-in synonymy mechanism that returns at most one sequence. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_query?mot_source=pat,ft&mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_query

For querying the classifications. Refer to HELP(cla_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [optional]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_cla_name=...A list of classification entry names to be included in the results (logical AND with the previous constraint). [optional]
not_cla_name=...A list of classification entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
desc_text=...A list of words to search for. [optional]
min_score=...A positive real number. [optional]
prop_key=...Limit the search to the sequence with the given property key(s). [optional]
prop_value=...Limit the search to entries with the supplied property value(s). The exhaustive list of all entries matching the criteria is returned. This is a major distinction from the built-in synonymy mechanism that returns at most one sequence. [optional]
ancestor=...A non-empty list of classification entry names or query identifiers that can return classification entries. [optional]
parent=...A non-empty list of classification entry names or query identifiers that can return classification entries. [optional]
descendant=...A non-empty list of classification entry names or query identifiers that can return classification entries. [optional]
child=...A non-empty list of classification entry names or query identifiers that can return classification entries. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_query?cla_source=taxid&cla_name=taxid:9606


action=hit_query

For querying the hit lists (sequence vs motif). Refer to HELP(hit_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [optional]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_seq_name=...A list of sequence entry names to be included in the results (logical AND with the previous constraint). [optional]
not_seq_name=...A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
mot_source=...A non-empty list of motif database names. [optional]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_mot_name=...A list of motif entry names to be included in the results (logical AND with the previous constraint). [optional]
not_mot_name=...A list of motif entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
hit_name=...A hit list given using query identifiers to be included in the results. [optional]
and_hit_name=...A hit list to be included in the results (logical AND with the previous constraint). [optional]
not_hit_name=...A hit list to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
signif=...A list of hit signif to be included in the results. [optional]
not_signif=...A list of hit signif to be excluded from the results. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hit_query?seq_source=sw&seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT&mot_source=pat,ft&mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=hat_query

For querying the 'hat' lists (sequence vs classification). Refer to HELP(hat_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [optional]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_seq_name=...A list of sequence entry names to be included in the results (logical AND with the previous constraint). [optional]
not_seq_name=...A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
cla_source=...A non-empty list of classification database names. [optional]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_cla_name=...A list of classification entry names to be included in the results (logical AND with the previous constraint). [optional]
not_cla_name=...A list of classification entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
hat_name=...A hat list given using query identifiers to be included in the results. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hat_query?seq_source=sw&seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT&cla_source=taxid&cla_name=taxid:9606


action=hot_query

For querying the 'hot' lists (motif vs classification). Refer to HELP(hot_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [optional]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_mot_name=...A list of motif entry names to be included in the results (logical AND with the previous constraint). [optional]
not_mot_name=...A list of motif entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
cla_source=...A non-empty list of classification database names. [optional]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
and_cla_name=...A list of classification entry names to be included in the results (logical AND with the previous constraint). [optional]
not_cla_name=...A list of classification entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
hot_name=...A hot list given using query identifiers to be included in the results. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hot_query?mot_source=pat,ft&mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin&cla_source=taxid&cla_name=taxid:9606


action=mom_query

Advanced query of the list of hits. Refer to HELP(mom_query) for details.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
metamotif=...Refer to the mom_query documentation for the complete syntax. [mandatory]
seq_source=...A non-empty list of sequence database names. [optional]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
not_seq_name=...A list of sequence entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
mot_source=...Scope of the ? operator: [optional]
mot_name=...Scope of the ? operator: A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [optional]
not_mot_name=...Scope of the ? operator: A list of motif entry names to be excluded from the results (logical NOT to restrict the two previous constraints). [optional]
signif=...Scope of the ? operator: A list of hit signif to be included in the results. [optional]
not_signif=...Scope of the ? operator: A list of hit signif to be excluded from the results. [optional]
-lim=...Maximum number of rows to be returned. [optional]
-ref=...A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mom_query?metamotif=((pat:THIOREDOXIN_1)/o/(ft:DOMAIN_Thioredoxin))&seq_source=sw&seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT&mot_source=pat,ft&mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=seq_fetch_name

Return the non-redundant list of sequence names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_name?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_name

Return the non-redundant list of motif names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_name?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_fetch_name

Return the non-redundant list of classification names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_fetch_name?cla_name=taxid:9606


action=seq_fetch_desc

Return the descriptive text attached to every sequence. This text can be search for using the desc_text constraint of the seq_query() method.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_desc?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_desc

Return the descriptive text attached to every motif. This text can be search for using the desc_text constraint of the mot_query() method.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_desc?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_fetch_desc

Return the descriptive text attached to every classification. This text can be search for using the desc_text constraint of the cla_query() method..

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_fetch_desc?cla_name=taxid:9606


action=seq_fetch_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_entry?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_entry?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_fetch_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_fetch_entry?cla_name=taxid:9606


action=seq_fetch_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_prop?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_prop?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=cla_fetch_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_name=...A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_fetch_prop?cla_name=taxid:9606


action=seq_fetch_fasta

Return the entry in FASTA format.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_fasta?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_fasta

Return the entry in FASTA format.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_fasta?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=seq_fetch_nr

Return the entry in FASTA format (non redundant).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_name=...A list of sequence entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_fetch_nr?seq_name=sw:THIO_RAT,sw:THIO_HUMAN,sw:PDI_WHEAT


action=mot_fetch_nr

Return the entry in FASTA format (non redundant).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_name=...A list of motif entry names (given explicitly, or implicitly using query identifiers) to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_fetch_nr?mot_name=pat:THIOREDOXIN_1,ft:DOMAIN_Thioredoxin


action=seq_dump_name

Return the non-redundant list of sequence names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_name?seq_source=sw


action=mot_dump_name

Return the non-redundant list of motif names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_name?mot_source=pat,ft


action=cla_dump_name

Return the non-redundant list of classification names.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_dump_name?cla_source=taxid


action=seq_dump_desc

Return the descriptive text attached to every sequence. This text can be search for using the desc_text constraint of the seq_query() method.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_desc?seq_source=sw


action=mot_dump_desc

Return the descriptive text attached to every motif. This text can be search for using the desc_text constraint of the mot_query() method.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_desc?mot_source=pat,ft


action=cla_dump_desc

Return the descriptive text attached to every classification. This text can be search for using the desc_text constraint of the cla_query() method..

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_dump_desc?cla_source=taxid


action=seq_dump_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_entry?seq_source=sw


action=mot_dump_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_entry?mot_source=pat,ft


action=cla_dump_entry

Return the non-redundant list of entry text.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_dump_entry?cla_source=taxid


action=seq_dump_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_prop?seq_source=sw


action=mot_dump_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_prop?mot_source=pat,ft


action=cla_dump_prop

Return the non-redundant list of synonyms and property.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
cla_source=...A non-empty list of classification database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/cla_dump_prop?cla_source=taxid


action=seq_dump_fasta

Return the entry in FASTA format.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_fasta?seq_source=sw


action=mot_dump_fasta

Return the entry in FASTA format.

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_fasta?mot_source=pat,ft


action=seq_dump_nr

Return the entry in FASTA format (non redundant).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
seq_source=...A non-empty list of sequence database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/seq_dump_nr?seq_source=sw


action=mot_dump_nr

Return the entry in FASTA format (non redundant).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
mot_source=...A non-empty list of motif database names. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/mot_dump_nr?mot_source=pat,ft


action=hit_fetch_simple

Retrieval of hit lists (sequence vs motif).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
hit_name=...A hit list given using query identifiers to be included in the results. [mandatory]
meta_hit_name=...A list of matches by a metamotif expression given using query identifiers. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hit_fetch_simple


action=hat_fetch_simple

Retrieval of 'hat' lists (sequence vs classification).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
hat_name=...A hat list given using query identifiers to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hat_fetch_simple


action=hot_fetch_simple

Retrieval of 'hot' lists (motif vs classification).

session_id=...A string returned by the connect action. [mandatory unless using cookie]
hot_name=...A hot list given using query identifiers to be included in the results. [mandatory]
-lim=...Maximum number of rows to be returned. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/hot_fetch_simple


action=query_list

Return summary information about the query stack

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/query_list


action=query_info

Return the details about the SQL statements: debugging!

session_id=...A string returned by the connect action. [mandatory unless using cookie]
query_id=...A list of query identifiers: A query identifier is a string that starts with "$" followed by a letter, and possibly more letter, digit or underscore. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/query_info?query_id=$QUERY_1


action=query_stat

Provides number(s) of rows for the different supported context(s)

session_id=...A string returned by the connect action. [mandatory unless using cookie]
query_id=...A list of query identifiers: A query identifier is a string that starts with "$" followed by a letter, and possibly more letter, digit or underscore. [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/query_stat?query_id=$QUERY_1


action=query_reset

Reset the query stack

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/query_reset


action=default_list

Return a few default settings

session_id=...A string returned by the connect action. [mandatory unless using cookie]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/default_list


action=default_set

Alter a few default settings

session_id=...A string returned by the connect action. [mandatory unless using cookie]
-lim=...Maximum number of rows to be returned. [optional]
-tim=...Default timeout in seconds [optional]
-format=...Either cli or xml - this option is irrelevant for the SOAP service. [optional]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/default_set


action=sticker

Prepare a comment to be attached to the next query

session_id=...A string returned by the connect action. [mandatory unless using cookie]
comment=...A sticky comment [mandatory]

Example: http://myhits.isb-sib.ch/cgi-bin/hk/restserv/sticker