CASBERT (Composite Annotation Search Using)

An interface to search for cellml, variables, images, and sedml.

Installation

pip install git+https://github.com/napakalas/casbert.git

Using

Searching

from casbert import Searcher
searcher = Searcher()

query = 'basolateral plasma membrane'

# searching variables
searcher.searchVariables(query=query, top=10, minSim=0.1)

# searching images
searcher.searchImages(query=query, top=10, minSim=0.1)

# searching components
searcher.searchComponents(query=query, top=10, minSim=0.1)

# searching cellml
searcher.searchCellmls(query=query, top=10, minSim=0.1)

# searching plots
searcher.searchPlots(query=query, top=10, minSim=0.1)

# searching sedml
searcher.searchSedmls(query=query, top=10, minSim=0.1)

Update indexes

from casbert import updateIndexes

# update using casbert_data.zip file
# the file is generated using casbert-indexer
file = './casbert_data.zip'
updateIndexes(file)

# update from server
updateIndexes()

Description

This package is used to search for variables, maths, biosimulation models, images, etc, in the Physiome Model Repository (PMR). The approach is named Compsite Annotation Search using BERT (CASBERT) which implements SentenceTransformer to represent entities and queries as embeddings. An entity is annotated with composite annotation to provide copmplete description.

Related repositories

CASBERT experiment

CASBERT index development

Search Engine Implementation

Search Engine Demo

BMSE: http://search.bm-se.cloud.edu.au/