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A browser-based visualization of chemistry papers, specifically morphology, material, and chemical data extracted from them. The UI was made with nanomaterial synthesis papers in mind.
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gold_data/materials_informatics_gold
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35k.json
99.json
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README.md
docker_build.sh
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gold_normalized.json
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README.md

Materials Informatics ChemVis (MICV)

Intro

  • A visual analytics system for the material informatics project

You can install this by installing python and installing the dependencies, or through Docker, which may be simpler.

Click on a dot in the lower left "Graph" section to start exploring.

Setup

1. Install

  • Have python and pip installed
  • install dependency: pip install -r requirements.txt

2. Run the visualization server

  • Start the server:
    python runServer.py
    • The default dataset is 35k.json. For others, run with python runServer.py --input FILE.json, where you substitute FILE.json. See the "Visualization Data" section for other input files.
  • Then open a browser at http://localhost:5010/ (in Chrome for the fastest performance)

Setup with Docker

1. Install

  • Install Docker
  • If OSX/Linux: run "./docker_build.sh" without the quotes. If Windows, run the last line in docker_build.sh

2. Run the visualization server

  • Similarily, if OSX/Linux: run "./docker_run.sh" without the quotes. If Windows, run last line in docker_run.sh.
    • Run "./docker_run.sh FILE.json" to chose another dataset besides the 35k dataset. See the regular Setup section for more details.
  • Then open a browser at http://localhost:5010/ (in Chrome for the fastest performance)

Visualization Data

  • 35k.json is data from our pipeline applied to the 35k papers downloaded from Elsevier.

  • 99.json is data from our pipeline applied to the 99 gold standard papers. The experimental sentence extraction step was substituted with the SME's annotated experimental sentence annotations.

  • gold_normalized.json is the chemical annotations from SMEs, normalized with our pipeline.

Gold Standard Data

Gold data is contained in the gold_data folder. The materials_informatics_gold_es_and_chems folder contains txt files containing the experimental sections of 99 gold standard papers, and ann files containing Brat formatted annotations of chemical entities. The gold_standard.json file contains the information of the materials_informatics_gold_es_and_chems files, as well as the morphology and composition annotation of the papers. These annotations are from subject matter experts.

Release

Release number LLNL-CODE-780105 ChemVis is distrubted under the MIT license.

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