Merge pull request #49 from NeotomaDB/dev

Merge Dev to Main for Initial Data Product Share with Sponsor

.gitignore

@@ -1,6 +1,5 @@
 # ignore files in models folder but keep .gitkeep
 models/ner/*
-results/ner/*
 !.gitkeep
 
 # exclude all txt files in data
@@ -11,6 +10,10 @@ data/**/*.json
 data/**/*.csv
 !data/entity-extraction/raw/taxa.csv
 
+# ignore files in models folder but keep .gitkeep
+models/ner/*
+!.gitkeep
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -4,68 +4,111 @@
 [![Issues][issues-shield]][issues-url]
 [![MIT License][license-shield]][license-url]
 
-# MetaExtractor: Finding Fossils in the Literature
-
-This project aims to identify research articles which are relevant to the [Neotoma Paleoecological Database](http://neotomadb.org) (Neotoma), extract data relevant to Neotoma from the article, and provide a mechanism for the data to be reviewed by Neotoma data stewards then submitted to Neotoma. It is being completed as part of the University of British Columbia (UBC) [Masters of Data Science (MDS) program](https://masterdatascience.ubc.ca/) in partnership with the [Neotoma Paleoecological Database](http://neotomadb.org).
+# **MetaExtractor: Finding Fossils in the Literature**
+
+This project aims to identify research articles which are relevant to the [_Neotoma Paleoecological Database_](http://neotomadb.org) (Neotoma), extract data relevant to Neotoma from the article, and provide a mechanism for the data to be reviewed by Neotoma data stewards then submitted to Neotoma. It is being completed as part of the _University of British Columbia (UBC)_ [_Masters of Data Science (MDS)_](https://masterdatascience.ubc.ca/) program in partnership with the [_Neotoma Paleoecological Database_](http://neotomadb.org).
+
+**Table of Contents**
+
+- [**MetaExtractor: Finding Fossils in the Literature**](#metaextractor-finding-fossils-in-the-literature)
+  - [**Article Relevance Prediction**](#article-relevance-prediction)
+  - [**Data Extraction Pipeline**](#data-extraction-pipeline)
+  - [**Data Review Tool**](#data-review-tool)
+  - [How to use this repository](#how-to-use-this-repository)
+    - [Entity Extraction Model Training](#entity-extraction-model-training)
+    - [Data Review Tool](#data-review-tool-1)
+    - [Data Requirements](#data-requirements)
+      - [Article Relevance Prediction](#article-relevance-prediction-1)
+      - [Data Extraction Pipeline](#data-extraction-pipeline-1)
+    - [Development Workflow Overview](#development-workflow-overview)
+    - [Analysis Workflow Overview](#analysis-workflow-overview)
+    - [System Requirements](#system-requirements)
+    - [**Directory Structure and Description**](#directory-structure-and-description)
+  - [**Contributors**](#contributors)
+    - [Tips for Contributing](#tips-for-contributing)
 
 There are 3 primary components to this project:
-1. **Article Relevance Prediction** - get the latest articles published, predict which ones are relevant to Neotoma and submit for processing
-2. **MetaData Extraction Pipeline** - extract relevant metadata from the article including geographic locations, taxa present, etc. 
-3. **Data Review Tool** - this takes the extracted data and allows a user to review and correct it for submission to Neotoma
+
+1. **Article Relevance Prediction** - get the latest articles published, predict which ones are relevant to Neotoma and submit for processing.
+2. **MetaData Extraction Pipeline** - extract relevant entities from the article including geographic locations, taxa, etc.
+3. **Data Review Tool** - this takes the extracted data and allows the user to review and correct it for submission to Neotoma.
 
 ![](assets/project-flow-diagram.png)
 
-## Article Relevance Prediction
+## **Article Relevance Prediction**
+
+The goal of this component is to monitor and identify new articles that are relevant to Neotoma. This is done by using the public [xDD API](https://geodeepdive.org/) to regularly get recently published articles. Article metadata is queried from the [CrossRef API](https://www.crossref.org/documentation/retrieve-metadata/rest-api/) to obtain data such as journal name, title, abstract and more. The article metadata is then used to predict whether the article is relevant to Neotoma or not.
+
+The model was trained on ~900 positive examples (a sample of articles currently contributing to Neotoma) and ~3500 negative examples (a sample of articles unrrelated or closely related to Neotoma). Logistic regression model was chosen for its outstanding performance and interpretability.
+
+Articles predicted to be relevant will then be submitted to the Data Extraction Pipeline for processing.
+
+![](assets/article_prediction_flow.png)
 
-The goal of this component is to monitor and identify new articles that are relevant to Neotoma. This is done by using the public [xDD API](https://geodeepdive.org/) to regularly get recently published articles. Article metadata is queried from the [CrossRef API](https://www.crossref.org/documentation/retrieve-metadata/rest-api/) to obtain data such as journal name, title, abstract and more. The article metadata is then used to predict whether the article is relevant to Neotoma or not. The predicted articles are then submitted to the MetaData Extraction Pipeline for processing.
+To run the Docker image for article relevance prediction pipeline, please refer to the instruction [here](docker/article-relevance/README.md)
 
-## MetaData Extraction Pipeline
+## **Data Extraction Pipeline**
 
-The predicted relevant articles have their full text provided by the xDD team and a custom trained Named Entity Recognition (NER) model is used to extract relevant data from the article. 
+The full text is provided by the xDD team for the articles that are deemed to be relevant and a custom trained **Named Entity Recognition (NER)** model is used to extract entities of interest from the article.
 
-The entities detected by this model are:
-- **AGE**: when historical ages are mentioned such as 1234 AD or 4567 BP (before present)
-- **TAXA**: plant or animal taxa names indicating what samples contained
-- **GEOG**: geographic coordinates indicating where samples were excavated from, e.g. 12'34"N 34'23"W
-- **SITE**: site names for where samples were excavated from
-- **REGION**: more general regions to provide context for where sites are located
-- **EMAIL**: researcher emails in the articles able to be used for follow-up contact
-- **ALTI**: altitudes of sites from where samples were excavated, e.g. 123 m a.s.l (above sea level)
+The entities extracted by this model are:
 
-The model was trained on ~40 existing Paleoecology articles manually annotated by the team consisting of ~60,000 tokens with ~4,500 tagged entities.
+- **SITE**: name of the excavation site
+- **REGION**: more general regions names to provide context for where sites are located
+- **TAXA**: plant or animal fossil names
+- **AGE**: historical age of the fossils, eg. 1234 AD, 4567 BP
+- **GEOG**: geographic coordinates indicating the location of the site, eg. 12'34"N 34'23"W
+- **EMAIL**: researcher emails referenced in the articles
+- **ALTI**: altitudes of sites, eg. 123 m a.s.l (above sea level)
 
-The trained model is available for inference and re-use on huggingface.co [here](https://huggingface.co/finding-fossils/metaextractor).
+The model was trained on ~40 existing Paleoecology articles manually annotated by the team consisting of **~60,000 tokens** with **~4,500 tagged entities**.
+
+The trained model is available for inference and further development on huggingface.co [here](https://huggingface.co/finding-fossils/metaextractor).
 ![](assets/hugging-face-metaextractor.png)
 
-## Data Review Tool
+## **Data Review Tool**
 
-Finally, the extracted data is loaded into the Data Review Tool where members of the Neotoma community can review the data and make any corrections necessary before submitting to Neotoma. The Data Review Tool is a web application built using the [Plotly Dash](https://dash.plotly.com/) framework. The tool allows users to view the extracted data, make corrections, and submit the data to be entered into Neotoma. 
+Finally, the extracted data is loaded into the Data Review Tool where members of the Neotoma community can review the data and make any corrections necessary before submitting to Neotoma. The Data Review Tool is a web application built using the [Plotly Dash](https://dash.plotly.com/) framework. The tool allows users to view the extracted data, make corrections, and submit the data to be entered into Neotoma.
 
 ![](assets/data-review-tool.png)
-## Contributors
 
-This project is an open project, and contributions are welcome from any individual.  All contributors to this project are bound by a [code of conduct](https://github.com/NeotomaDB/MetaExtractor/blob/main/CODE_OF_CONDUCT.md).  Please review and follow this code of conduct as part of your contribution.
+## How to use this repository
 
-The UBC MDS project team consists of:
-- Ty Andrews
-- Kelly Wu
-- Jenit Jain
-- Shaun Hutchinson
+First, begin by installing the requirements and Docker if not already installed ([Docker install instructions](https://docs.docker.com/get-docker/))
 
-Sponsors from Neotoma supporting the project are:
-* [![ORCID](https://img.shields.io/badge/orcid-0000--0002--7926--4935-brightgreen.svg)](https://orcid.org/0000-0002-7926-4935) [Socorro Dominguez Vidana](https://ht-data.com/)
-* [![ORCID](https://img.shields.io/badge/orcid-0000--0002--2700--4605-brightgreen.svg)](https://orcid.org/0000-0002-2700-4605) [Simon Goring](http://www.goring.org)
+```bash
+pip install -r requirements.txt
+```
 
-### Tips for Contributing
+A conda environment file will be provided in the final release.
 
-Issues and bug reports are always welcome.  Code clean-up, and feature additions can be done either through pull requests to [project forks](https://github.com/NeotomaDB/MetaExtractor/network/members) or [project branches](https://github.com/NeotomaDB/MetaExtractor/branches).
+### Entity Extraction Model Training
 
-All products of the Neotoma Paleoecology Database are licensed under an [MIT License](LICENSE) unless otherwise noted.
+The Entity Extraction Models can be trained using the HuggingFace API by following the instructions in the [Entity Extraction Training README](src/entity_extraction/training/hf_token_classification/README.md).
 
-## How to use this repository
+The spaCy model training documentation is a WIP.
 
-WIP
+### Data Review Tool
+
+The Data Review Tool can be launched by running the following command from the root directory of this repository:
+
+```bash
+docker-compose up --build data-review-tool
+```
+
+Once the image is built and the container is running, the Data Review Tool can be accessed at http://localhost:8050/. There is a sample "extracted entities" JSON file provided for demo purposes.
+
+### Data Requirements
 
+Each of the components of this project have different data requirements. The data requirements for each component are outlined below.
+
+#### Article Relevance Prediction
+
+The article relevance prediction component requires a list of journals that are relevant to Neotoma. This dataset used to train and develop the model is available for download HERE. TODO: Setup public link for data download from project GDrive.
+
+#### Data Extraction Pipeline
+
+As the full text articles provided by the xDD team are not publicly available we cannot create a public link to download the labelled training data. For access requests please contact Ty Andrews at ty.elgin.andrews@gmail.com.
 
 ### Development Workflow Overview
 
@@ -79,16 +122,16 @@ WIP
 
 WIP
 
-### Data Requirements
-
-WIP
-
-### Directory Structure and Description
+### **Directory Structure and Description**
 
 ```
 ├── .github/                            <- Directory for GitHub files
 │   ├── workflows/                      <- Directory for workflows
 ├── assets/                             <- Directory for assets
+├── docker/                             <- Directory for docker files
+│   ├── article-relevance/              <- Directory for docker files related to article relevance prediction
+│   ├── data-review-tool/               <- Directory for docker files related to data review tool
+│   ├── entity-extraction/              <- Directory for docker files related to named entity recognition
 ├── data/                               <- Directory for data
 │   ├── entity-extraction/              <- Directory for named entity extraction data
 │   │   ├── raw/                        <- Raw unprocessed data
@@ -113,13 +156,35 @@ WIP
 ├── src/                                <- Directory for source code
 │   ├── entity_extraction/              <- Directory for named entity recognition code
 │   ├── article_relevance/              <- Directory for article relevance prediction code
-│   └── data_review_tool/               <- Directory for data review tool code             
+│   └── data_review_tool/               <- Directory for data review tool code
 ├── reports/                            <- Directory for reports
 ├── tests/                              <- Directory for tests
 ├── Makefile                            <- Makefile with commands to perform analysis
 └── README.md                           <- The top-level README for developers using this project.
 ```
 
+## **Contributors**
+
+This project is an open project, and contributions are welcome from any individual. All contributors to this project are bound by a [code of conduct](https://github.com/NeotomaDB/MetaExtractor/blob/main/CODE_OF_CONDUCT.md). Please review and follow this code of conduct as part of your contribution.
+
+The UBC MDS project team consists of:
+
+- **Ty Andrews**
+- **Kelly Wu**
+- **Jenit Jain**
+- **Shaun Hutchinson**
+
+Sponsors from Neotoma supporting the project are:
+
+- [![ORCID](https://img.shields.io/badge/orcid-0000--0002--7926--4935-brightgreen.svg)](https://orcid.org/0000-0002-7926-4935) [Socorro Dominguez Vidana](https://ht-data.com/)
+- [![ORCID](https://img.shields.io/badge/orcid-0000--0002--2700--4605-brightgreen.svg)](https://orcid.org/0000-0002-2700-4605) [Simon Goring](http://www.goring.org)
+
+### Tips for Contributing
+
+Issues and bug reports are always welcome. Code clean-up, and feature additions can be done either through pull requests to [project forks](https://github.com/NeotomaDB/MetaExtractor/network/members) or [project branches](https://github.com/NeotomaDB/MetaExtractor/branches).
+
+All products of the Neotoma Paleoecology Database are licensed under an [MIT License](LICENSE) unless otherwise noted.
+
 [contributors-shield]: https://img.shields.io/github/contributors/NeotomaDB/MetaExtractor.svg?style=for-the-badge
 [contributors-url]: https://github.com/NeotomaDB/MetaExtractor/graphs/contributors
 [forks-shield]: https://img.shields.io/github/forks/NeotomaDB/MetaExtractor.svg?style=for-the-badge
@@ -129,4 +194,4 @@ WIP
 [issues-shield]: https://img.shields.io/github/issues/NeotomaDB/MetaExtractor.svg?style=for-the-badge
 [issues-url]: https://github.com/NeotomaDB/MetaExtractor/issues
 [license-shield]: https://img.shields.io/github/license/NeotomaDB/MetaExtractor.svg?style=for-the-badge
-[license-url]: https://github.com/NeotomaDB/MetaExtractor/blob/master/LICENSE.txt
+[license-url]: https://github.com/NeotomaDB/MetaExtractor/blob/master/LICENSE.txt