Morre

Morre – Model Ranked Retrieval Engine

Morre is an Information Retrieval System to search for computational models and related data. It is based on Neo4J and Lucene. Supported model formats are currently SBML and CellML. You can search for models or related persons, publications and annotations.

Here, the Web Service of Morre is described – try it!

For this showcase we use cURL, however feel free to use any tool able to handle HTTP Get and POST requests.

In general, the link structure follows the pattern

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http://morre.sems.uni-rostock.de:7474/morre/query/[query type]/

You can replace query type with:

  • model_query
  • simple_cellml_model_query
  • cellml_model_query
  • simple_sbml_model_query
  • sbml_model_query
  • person_model_query
  • person_query
  • publication_model_query
  • publication_query
  • annotation_model_query
  • annotation_query

For each query type a Get and POST request is possible. The Get request will return a JSON object holding all available features for the particular query. In case of the cellml_model_query the request is:

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curl -X GET http://morre.sems.uni-rostock.de:7474/morre/query/cellml_model_query/ -H "Content-Type: text/plain"

The returned JSON object is:

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["ID","NAME","COMPONENT","VARIABLE","CREATOR","AUTHOR"]

Now we can setup a query using POST and a JSON object:

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curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/cellml_model_query/ -H "Content-Type: application/json" -d '{"features":["NAME","ID","COMPONENT"], "keywords":["tyson","cell cycle","cdc2"]}'

As a result a JSON object is returned containing the retrieved models and according scores.

Also, try the following queries to get an impression of the capabilities:

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curl -X GET http://morre.sems.uni-rostock.de:7474/morre/query/cellml_model_query/ -H "Content-Type: text/plain"

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/simple_cellml_model_query/ -H "Content-Type: application/json" -d '{"keyword":"novak"}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/simple_cellml_model_query/ -H "Content-Type: application/json" -d '{"keyword":"novak", "topn":"3"}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/cellml_model_query/ -H "Content-Type: application/json" -d '{"features":["NAME","ID","COMPONENT"], "keywords":["novak","novak","sodium_current_h_gate"]}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/cellml_model_query/ -H "Content-Type: application/json" -d '{"features":["NAME","ID","COMPONENT"], "keywords":["novak","novak","sodium_current_h_gate"],"topn":"3"}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/person_model_query/ -H "Content-Type: application/json" -d '{"features":["FAMILYNAME"], "keywords":["Lloyd"]}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/publication_model_query/ -H "Content-Type: application/json" -d '{"features":["TITLE"], "keywords":["Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump"]}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/person_query/ -H "Content-Type: application/json" -d '{"features":["GIVENNAME"], "keywords":["Sulman"]'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/publication_query/ -H "Content-Type: application/json" -d '{"features":["TITLE"], "keywords":["Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump"]}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/annotation_model_query/ -H "Content-Type: application/json" -d '{"keyword":"This study investigates the reverse mode of the Na/glucose cotransporter SGLT1. In giant excised inside-out membrane patches from Xenopus laevis oocytes expressing rabbit SGLT1, application of alpha-methyl D"}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/annotation_query/ -H "Content-Type: application/json" -d '{"keyword":"This study investigates the reverse mode of the Na/glucose cotransporter SGLT1. In giant excised inside-out membrane patches from Xenopus laevis oocytes expressing rabbit SGLT1, application of alpha-methyl D"}'

curl -X POST http://morre.sems.uni-rostock.de:7474/morre/query/model_query/ -H "Content-Type: application/json" -d '{"keyword":"novak sodium model math channel"}'