API documents v0.1

Jorge edited this page Jan 4, 2018 · 125 revisions

NOTE : This is an beta API version. We thank you for your understanding and appreciate your feedback


API documents v0.1

API to analyze, upload, and/or download documents and their annotations. These 3 possible effects are transparent to the user and are unified into one single API. Additionally, you can use the same API to delete documents.

Authentication

The current API supports Basic Authentication. Note that the username and password are secured via an https connection.

For free requests, with some limitations, you can leave the username:password combination empty.

Parameters

The following are the supported parameters in this API version. Those marked as PUT can be sent in a PUT request and must be contained in the request body. In addition, those marked as GET can be sent in GET or PUT requests and be contained in the body (if PUT) or directly in the URL (which is limited to 2000 characters).

Additionally, those parameters marked with DELETE can be sent in an http DELETE request for the the deletion of documents. Using DELETE, the output is a single integer indicating the number of effectively deleted documents -- the output parameter is discarded.

Those parameters with defined value ... represent non-empty value lists. Those with defined value . represent single values. In particular, all API submissions can be for 1 or more documents (non-empty list). In practice, however, different output formats allow either only 1 document or multiple ones.

  • Input (each subgroup is incompatible with each other. See below for documentation):

    • By id:
      • (GET+DELETE) idType=. (defaults to tagtogID)
      • (GET+DELETE) ids=... (comma-separated list of ids, all of the same type. For DELETE to work, the idType must be tagtogID)
    • (PUT) text=. (free text / string)
    • (GET) url=. (or synonym target=.) (url pointing to a document resource)
    • (PUT) files=...
    • (GET+DELETE) search= see search options. Compatible with the outputs:
      • search (default)
      • authors
      • csv (in this case, the query is ignored & all documents are returned)
  • (GET) ontologies=... -- comma-separated list of the names of your project's ontologies/dictionaries to use for the document entity tagging; defaults to ontologies=*, meaning all project-defined ontologies/dictionaries. Example: ontologies=City,Name,SwissProt. If empty (as in ontologies=), no analysis is performed, which effectively serves the purpose of uploading documents as is. Note: you can include (the name of) your own dictionaries and also the tagtog-ml supported ontologies.

  • (GET) output=. (defaults to visualize -- See below for documentation)

Optional Parameters

  • Project specific:

    • (GET) owner=. (defaults to the username sending the request)
    • (GET) member=. (defaults to master, aka project official annotations. Otherwise this is only applicable if the project has multiple team members)
    • (GET) folder=. (defaults to pool; possible values: {pool, test})
  • Other:

    • (GET) page=. (Number: page number in a paginated search; see search parameter)
    • (GET) part=. (specific document part/section as referenced by the the element if of the html) -- Note: currently it works only with outputs html and txt (and their synonyms)
    • (GET) ann=. (specific annotation as uniquely identified in the ann.json) -- Note: currently it works only with output json-ld

Parameters planned for a next API version

  • no specific plans

Input

idType

Possible values are:

  • tagtogID -- tagtog-internal document id or docid. Its use implicitly means that the document already exists in the associated project.
  • PMID -- PubMed ID
  • PMCID -- PubMed Central ID

files

Any file accepted by tagtog at the time of the request or as limited by the current API version, if any. See input formats.

output Formats

General description of the output formats accepted here: output formats

The output format can be specified with the output parameter. Formats prefixed with 1 support one document only. In practice, for these outputs you must submit multiple API requests to obtain multiple document results. Those formats prefixed with n support multiple documents. In practice, for these outputs a single API request suffices to obtain results of multiple documents.

  • (1) visualize -- choose to visualize the document resource returning the web page directly (web or web-editor-only if the User Agent is a recognized browser and a tagtog project information was given, i.e. web, or, respectively, no tagtog project was given, i.e., web-editor-only) or otherwise return the weburl (typically, the User Agent will be a command line program)
  • (1) web -- visual representation of the document and its annotations on the tagtog web interface (HTML page)
  • (1) web-editor-only -- analogously as web, yet without the information of a tagtog project, i.e., only the document editor is shown.
  • (1) weburl -- url of the document resource and its annotations pointing to the tagtog web interface
  • (n) null -- special output to signify that no document output is desired. A JSON response of the request will be returned instead. Note, you can use null for uploading multiple files at once.
  • (1) ann.json -- annotations part of the anndoc format
  • (1) html or xml -- content part of the anndoc format
  • (1) txt or text -- document content in plain text
  • (n) tsv-- see here (you must be logged in tagtog). Note: doesn't work at the moment
  • (n) search -- JSON format for a search's results. Compatible only with the input search
  • (n) csv -- list of the project's documents and their master (official) annotation status'. Note: currently it works only with input search=*
  • (1) pubannotation -- See here
  • (1) docjson -- experimental output
  • (1) json-ld -- See here
  • (1) bioc -- See here
  • (n) authors -- (json format) it will retrieve a ranking with list of authors that has written the documents found with the parameter search. authors-1 will limit the ranking to the author who wrote the largest amount of publications. You can use authors-2, authors-3, ..., authors-200. By default 20. [See the output format here] (https://github.com/tagtog/tagtog-doc/wiki/Authors-view-example)

Note: all output formats are returned in their latest format versions. The format versions cannot be chosen.


Examples

Upload (files) & Search & Download

🐍 python

Use the official tagtog script 😀

Annotate a web site

Upload and annotate URL.

💻 curl

Please remember to use basic authentication.

curl -u yourUsername:yourPassword 'https://www.tagtog.net/api/0.1/documents?project=yourprojectname&owner=yourusername&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fprojects%2Fgap%2Fcgi-bin%2Fstudy.cgi%3Fstudy_id%3Dphs000980.v1.p1&output=ann.json'

🌐browser

Remember you need to be logged in if you want to use the API through the browser.

https://www.tagtog.net/api/0.1/documents?project=yourprojectname&owner=yourusername&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fprojects%2Fgap%2Fcgi-bin%2Fstudy.cgi%3Fstudy_id%3Dphs000980.v1.p1&output=visualize

Annotate one document with PMID (or PMCID)

Upload and annotate a PubMed article using its PMID

💻 curl

Please remember to use basic authentication.

curl -u yourUsername:yourPassword 'https://www.tagtog.net/api/0.1/documents?project=yourprojectname&owner=yourusername&idType=PMID&ids=23596191&output=bioc'

🌐browser

Remember you need to be logged in if you want to use the API through the browser.

https://www.tagtog.net/api/0.1/documents?project=yourprojectname&owner=yourusername&idType=PMID&ids=23596191&output=ann.json

Annotate plain text

Upload and annotate plain text.

💻 curl

Please remember to use basic authentication.

curl -u yourUsername:yourPassword -X PUT -d 'text=Antibody-dependent cellular cytotoxicity (ADCC), a key effector function for the clinical effectiveness of monoclonal antibodies, is triggered by the engagement of the antibody Fc domain with the Fcγ receptors expressed by innate immune cells such as natural killer (NK) cells and macrophages. Here, we fused cancer cell-binding peptides to the Fc domain of human IgG1 to engineer novel peptide-Fc fusion proteins with ADCC activity' 'https://www.tagtog.net/api/0.1/documents?project=yourprojectname&owner=yourusername&output=pubannotation'

🐍 python

#pip install requests
import requests

url = 'https://www.tagtog.net/api/0.1/documents'
auth = requests.auth.HTTPBasicAuth(username='<your_username>', password='<your_password>')
params = {'project':'<your_project>', 'owner':'<your_username>', 'output':'ann.json'}
text = 'Antibody-dependent cellular cytotoxicity (ADCC), a key effector function for the clinical effectiveness of monoclonal antibodies'
payload = {'text': text}
response = requests.put(url, params=params, auth=auth, data=payload)
print(response, response.text)

Search documents in a project

💻 curl

The following call will retrieve the documents matching the search string, in this case * represents all documents.

curl -u yourUsername:yourPassword 'https://www.tagtog.net/api/0.1/documents?project=project_name&search=*'

The format of the output: search format To build the search string: search parameter


Get documents already uploaded

You need the Id of the document before you get it. If you don't have this Id, you can find it using the search feature. In the next example, we use this id to get the document in ann.json format.

curl -u yourUsername:yourPassword 'https://www.tagtog.net/api/0.1/documents?project=project_name&ids=aVTjgPL0x5m_xgJr3qcpfXcSoY_q-text&output=ann.json'

Delete all documents in a project

💻 curl

curl -u yourUsername:yourPassword -X DELETE 'https://www.tagtog.net/api/0.1/documents?project=yourProject&search=*'

Similarly, fine-tune the search parameter to delete only those documents returned by the search; search=* finds all and therefore the DELETE call deletes all documents.

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