update readme

LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2024 Jonas Renault
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,5 +1,8 @@
 # CPREx - Chemical Properties Relation Extraction
 
+[![License](https://img.shields.io/badge/License-MIT-yellow)](LICENSE)
+![python_version](https://img.shields.io/badge/Python-%3E=3.10-blue)
+
 CPREx is an end to end tool for Named Entity Recognition (NER) and Relation Extraction (RE) specifically designed for chemical compounds and their properties. The goal of the tool is to identify, extract and link chemical compounds and their properties from scientific literature. For ease of use, CPREx provides a custom [spacy](https://spacy.io/) pipeline to perform NER and RE.
 
 The pipeline performs the following steps
@@ -10,18 +13,88 @@ flowchart LR
     fetch PDF articles
     from online archives`")
     parser("`**parser**
-    Extract text from PDF`")
+    Extract text
+    from PDF`")
     crawler --> parser
     parser --> ner
     ner("`**NER**
-    extract named entities`")
-    ner --> chem[Chem] --> rel
-    ner --> prop[Property] --> rel
-    ner --> quantity[Value] --> rel
+    extract named
+    entities`")
+    ner --> chem["`**Chem**
+    *1,3,5-Triazine*
+    *Zinc bromide*
+    *C₃H₄N₂*`"] --> rel
+    ner --> prop["`**Property**
+    *fusion enthalpy*
+    *Tc*`"] --> rel
+    ner --> quantity["`**Value**
+    *169°C*
+    *21.49 kJ/mol*`"] --> rel
     rel("`**Relation Extraction**
     link entities`")
     rel --> res
     res("`**(Chem, Property, Value)**
-    *2,2'-Binaphthalene*, ΔHfus, 38.9 kJ/mol`")
+    *2,2'-Binaphthalene, ΔHfus, 38.9 kJ/mol*`")
+```
+
+## Installation
+
+CPREx works with a recent version of python (**>=python 3.11**). Make sure to install CPREx in a virtual environment of your choice.
+
+CPREx depends on [GROBID](https://github.com/kermitt2/grobid) and its extension [grobid-quantities](https://github.com/lfoppiano/grobid-quantities) for parsing PDF documents and extracting quantities from their text. In order to install and run GROBID, a JDK must also be installed on your machine. [GROBID currently supports](https://grobid.readthedocs.io/en/latest/Install-Grobid/) JDKs from **1.11 to 1.17**.
+
+### Install via PyPI
+
+You can install CPREx directly with pip:
+
+```console
+pip install cprex
+```
+
+### Install from github
+
+This installation is recommended for users who want to customize the pipeline or train some models on their own dataset.
+
+Clone the repository and install the project in your python environment.
+
+```console
+git clone [email protected]:jonasrenault/cprex.git
+cd cprex
+pip install --editable .
+```
+
+Any modifications you make to the cprex codebase will be immediatly reflected thanks to the `--editable` option.
 
+### Install grobid and models
+
+#### Installing and running grobid
+
+CPREx depends on [GROBID](https://github.com/kermitt2/grobid) and its extension [grobid-quantities](https://github.com/lfoppiano/grobid-quantities) for parsing PDF documents and extracting quantities from their text.
+
+For convenience, CPREx provides a command line interface (CLI) to install grobid and start a grobid server.
+
+Run
+
+```console
+cprex install-grobid
 ```
+
+to install a grobid server and the grobid-quantities extension (by default, grobid and models required by CPREx are installed in a `.cprex` directory in your home directory).
+
+Run
+
+```console
+cprex start-grobid
+```
+
+to start a grobid server and enable parsing of PDF documents from CPREx.
+
+#### Installing NER et REL models
+
+To perform Named Entity Recognition of chemical compounds and Relation Extraction, CPREx requires some pretrained models. These models can be installed by running
+
+```console
+cprex install-models
+```
+
+This will install a PubmedBert model finetuned on the NLM-CHEM corpus for extraction of chemical named entities. This model was finetuned by the [BioCreative VII track](https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-2/).