SourceData SmartTag web tool

SmartTag provides methods to tag text from figure legends based on the SourceData model.

Base URL

https://smtag.sourcedata.io/api/v1/

Complete annotation

Method to perform the complete tagging of a text, including panel segmentation, typed entity tagging and role prediction.

Request: GET | POST /smtag

URL Params:

text=[string] (required): the text to process
format=['html' (default) |'xml'] (optional): the format of the output.
tag=['sd-tag' (default)|'sd-pretag']: the element/class used to tag entities; set to ‘sd-tag’ by default.

Examples:

$ curl 'https://smtag.sourcedata.io/api/v1/smtag?text=A%20Creb1-/-%20cell.&format=xml&tag=sd-pretag'

<smtag><sd-panel><sd-pretag type="organism" type_score="62">A</sd-pretag> <sd-pretag type="geneprod" role="intervention" type_score="96" role_score="91">Creb1</sd-pretag>-/- cell.</sd-panel></smtag>

$ curl 'https://smtag.sourcedata.io/api/v1/smtag?text=A%20Creb1-/-%20cell.&format=html'

<ul><li class="sd-panel">A <span class="sd-tag geneprod type_score_9 intervention role_score_8">Creb1</span>-/- cell.</li></ul>

Tag entities only

Method to tag entities.

Request: GET | POST /entity

URL Params:

text=[string] (required): the text to process
format=['html' (default) |'xml'] (optional): the format of the output.
tag=['sd-tag' (default)|'sd-pretag']: the element/class used to tag entities; set to ‘sd-tag’ by default.

Examples:

$ curl 'https://smtag.sourcedata.io/api/v1/entity?text=A%20Creb1-/-%20cell.&format=xml&tag=sd-pretag'

<smtag>A <sd-tag type="geneprod" type_score="68">Jun</sd-tag>-/- cell.</smtag>

curl 'https://smtag.sourcedata.io/api/v1/entity?text=A%20Creb1-/-%20cell.&format=html'

A <span class="sd-tag geneprod type_score_9">Creb1</span>-/- cell.

Role prediction only

Method to predict the roles from pretagged content.

Request: GET | POST /role

URL Params:

pretagged=[xml_string] (required): the pretagged content as xml
tag=[sd-tag|sd-pretag (default)] (optional): the element that needs to be updated; set to ‘sd-pretag’ by default

Examples:

curl -G 'https://smtag.sourcedata.io/api/v1/role' --data-urlencode 'pretagged=<something><sd-tag type="geneprod">Atg4</sd-tag> levels in <sd-pretag type="geneprod" category="" type_score="68" irrelevant_attr="hello">Creb1</sd-pretag>-/- cell.</something>'

<something><sd-tag type='geneprod'>Atg4</sd-tag> levels in <sd-pretag irrelevant_attr='hello' type_score='68' role='intervention' type='geneprod' category=''>Creb1</sd-pretag>-/- cell.</something>

Note: only elements are updated.

curl -G 'https://smtag.sourcedata.io/api/v1/role' --data-urlencode 'pretagged=<something><sd-tag type="geneprod">Atg4</sd-tag> levels in <sd-pretag type="geneprod" type_score="68" irrelevant_attr="hello">Creb1</sd-pretag>-/- cell.</something>' --data 'tag=sd-tag'

<something><sd-tag type='geneprod' role='assayed'>Atg4</sd-tag> levels in <sd-pretag irrelevant_attr='hello' type='geneprod' type_score='68'>Creb1</sd-pretag>-/- cell.</something>

Note: only sd-tag is updated because of the tag=sd-tag parameter

Notes:

By default, only <sd-pretag category=""> elements are updated, the rest of the elements are left untouched
If another element is specified by the tag parameter, only these elements are updated (but without any constraint on attributes)
The attribute @role with the default value @role='component' is added to all the updated elements.
For the updated elements that have @type='geneprod' or @type='molecule', the attribute @role='intervention' or @role='assayed' may be added based on the predicted role.

Tag entities and predict roles

Method to tag entities.

Request: GET | POST /tag

URL Params:

text=[string] (required): the text to process
format=['html' (default) |'xml'] (optional): the format of the output.
tag=[sd-tag (default)|sd-pretag] (optional): the element/class used to tag entities; set to ‘sd-tag’ by default.

Examples:

$ curl 'https://smtag.sourcedata.io/api/v1/tag?text=A%20Creb1-/-%20cell.&format=xml'

smtag>A <sd-tag type="geneprod" role="intervention" type_score="95" role_score="75">Creb1</sd-tag>-/- cell.</smtag>

$ curl 'https://smtag.sourcedata.io/api/v1/tag?text=A%20Creb1-/-%20cell.&format=html&tag=pre-tag'

A <span class="pre-tag geneprod type_score_9 intervention role_score_9">Creb1</span>-/- cell.

Segment panels only

Method to split the text of a figure legend into individual panels.

Request: GET | POST /panelize

URL Params:

text=[string] (required): the text to process
format=['html' (default) |'xml'] (optional): the format of the output.

Examples:

https://smtag.sourcedata.io/api/v1/panelizer?text=(A)%20This%20is%20a%20panel.%20(B)%20This%20is%20differnt%20from%20(A)%20or%20(C).%20(C,%20D)%20The%20rest.&format=xml

<smtag>
	<sd-panel>(A) This is a panel.</sd-panel>
	<sd-panel>(B) This is differnt from (A) or (C).</sd-panel>
	<sd-panel>(C, D) The rest.</sd-panel>
</smtag>

https://smtag.sourcedata.io/api/v1/panelizer?text=(A)%20This%20is%20a%20panel.%20(B)%20This%20is%20differnt%20from%20(A)%20or%20(C).%20(C,%20D)%20The%20rest.&format=html

<ul>
    <li class="sd-panel">(A) This is a panel. </li>
    <li class="sd-panel">(B) This is differnt from (A) or (C). </li>
    <li class="sd-panel">(C, D) The rest.</li>
</ul>