Update README.md

README.md

@@ -1,3 +1,190 @@
 ---
 license: mit
+language:
+- en
+tags:
+- biology
+- protein structure
+- token classification
 ---
+
+## Overview
+
+This data was used to evaluate the two models below to decide whether convergence was reached.
+https://huggingface.co/PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v2.1
+https://huggingface.co/PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1
+
+There are 20 different entity types in this dataset:
+"bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", 
+"mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name",
+"residue_name_number","residue_number", "residue_range", "site", "species", "structure_element",
+"taxonomy_domain"
+
+Annotation was carried out with the free annotation tool TeamTat (https://www.teamtat.org/) and
+documents were downloaded as BioC XML before converting them to IOB, annotation only JSON and CSV format. 
+
+The number of annotations and sentences in each file is given below:
+
+| document ID | number of annotations in BioC XML | number of annotations in IOB/JSON/CSV | number of sentences |
+| --- | --- | --- | --- |
+| PMC5173035 | 885 | 885 | 195 |
+| PMC4993997 | 1052 | 1051 | 217 |
+| PMC5014086 | 676 | 676 | 136 |
+| PMC5063996 | 1048 | 1046 | 243 |
+| PMC4980666 | 669 | 669 | 164 |
+| PMC4817029 | 897 | 897 | 180 |
+| PMC5012862 | 2203 | 2202 | 438 |
+| PMC4981400 | 570 | 570 | 121 |
+| PMC4806292 | 760 | 760 | 167 |
+| PMC5603727 | 1353 | 1353 | 240 |
+| total | 10113 | 10109 | 2101 |
+
+Documents and annotations are easiest viewed by using the BioC XML files and opening
+them in free annotation tool TeamTat (https://www.teamtat.org/). More about the BioC
+format can be found here: https://bioc.sourceforge.net/
+
+## Raw BioC XML files
+These are the raw, un-annotated XML files for the publications in the dataset in BioC format.
+The files are found in the directory: "raw_BioC_XML"
+There is one file for each document and they follow standard naming
+"unique PubMedCentral ID"_raw.xml
+
+## Annotations in IOB format
+The IOB formated files can be found in the directory: "annotation_IOB". There is one file for each
+document in the dataset and they all follow the naming "unique PubMedCentral ID".tsv.
+
+
+## Annotations in BioC JSON
+The BioC formated JSON files of the publications have been downloaded from the annotation
+tool TeamTat. The files are found in the directory: "annotated_BioC_JSON"
+There is one file for each document and they follow standard naming
+"unique PubMedCentral ID"_ann.json
+
+Each document JSON contains the following relevant keys:
+* "sourceid" --> giving the numerical part of the unique PubMedCentral ID
+* "text" --> containing the complete raw text of the publication as a string
+* "denotations" --> containing a list of all the annotations for the text
+
+Each annotation is a dictionary with the following keys:
+* "span" --> gives the start and end of the annotatiom span defined by sub keys:
+  * "begin" --> character start position of annotation
+  * "end" --> character end position of annotation
+* "obj" --> a string containing a number of terms that can be separated by ","; the order
+            of the terms gives the following: entity type, reference to ontology, annotator,
+            time stamp
+* "id" --> unique annotation ID
+
+Here an example:
+```json
+[{"sourceid":"4784909",
+  "sourcedb":"",
+  "project":"",
+  "target":"",
+  "text":"",
+  "denotations":[{"span":{"begin":24,
+                          "end":34},
+                  "obj":"chemical,CHEBI:,melaniev@ebi.ac.uk,2023-03-21T15:19:42Z",
+                  "id":"4500"},
+                 {"span":{"begin":50,
+                          "end":59},
+                  "obj":"taxonomy_domain,DUMMY:,melaniev@ebi.ac.uk,2023-03-21T15:15:03Z",
+                  "id":"1281"}]
+  }
+]
+```
+
+
+## Annotations in BioC XML
+The BioC formated XML files of the publications have been downloaded from the annotation
+tool TeamTat. The files are found in the directory: "annotated_BioC_XML"
+There is one file for each document and they follow standard naming
+"unique PubMedCentral ID_ann.xml
+
+The key XML tags to be able to visualise the annotations in TeamTat as well as extracting
+them to create the training data are "passage" and "offset". The "passage" tag encloses a
+text passage or paragraph to which the annotations are linked. "Offset" gives the passage/
+paragraph offset and allows to determine the character starting and ending postions of the
+annotations. The tag "text" encloses the raw text of the passage.
+
+Each annotation in the XML file is tagged as below:
+* "annotation id=" --> giving the unique ID of the annotation
+* "infon key="type"" --> giving the entity type of the annotation
+* "infon key="identifier"" --> giving a reference to an ontology for the annotation
+* "infon key="annotator"" --> giving the annotator
+* "infon key="updated_at"" --> providing a time stamp for annotation creation/update
+* "location" --> start and end character positions for the annotated text span
+  * "offset" --> start character position as defined by offset value
+  * "length" --> length of the annotation span; sum of "offset" and "length" creates
+                 the end character position
+
+Here is a basic example of what the BioC XML looks like. Additional tags for document
+management are not given. Please refer to the documenttation to find out more.
+
+```xml
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE collection SYSTEM "BioC.dtd">
+<collection>
+  <source>PMC</source>
+  <date>20140719</date>
+  <key>pmc.key</key>
+  <document>
+    <id>4784909</id>
+    <passage>
+      <offset>0</offset>
+      <text>The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle</text>
+      <annotation id="4500">
+        <infon key="type">chemical</infon>
+        <infon key="identifier">CHEBI:</infon>
+        <infon key="annotator">melaniev@ebi.ac.uk</infon>
+        <infon key="updated_at">2023-03-21T15:19:42Z</infon>
+        <location offset="24" length="10"/>
+        <text>Coenzyme A</text>
+      </annotation>
+    </passage>
+  </document>
+</collection>
+```
+
+
+## Annotations in CSV
+The annotations and the relevant sentences they have been found in have also been made
+available as tab-separated CSV files, one for each publication in the dataset. The files can
+be found in directory "annotation_CSV". Each file is named as "unique PubMedCentral ID".csv.
+
+The column labels in the CSV files are as follows:
+* "anno_start" --> character start position of the annotation
+* "anno_end" --> character end position of the annotation
+* "anno_text" --> text covered by the annotation
+* "entity_type" --> entity type of the annotation
+* "sentence" --> sentence text in which the annotation was found
+* "section" --> publication section in which the annotation was found
+
+
+## Annotations in JSON
+A combined JSON file was created only containing the relevant sentences and associated
+annotations for each publication in the dataset. The file can be found in directory
+"annotation_JSON" under the name "annotations.json".
+
+The following keys are used:
+* "PMC4850273" --> unique PubMedCentral of the publication
+* "annotations" --> list of dictionaries for the relevant, annotated sentences of the
+                    document; each dictionary has the following sub keys
+  * "sid" --> unique sentence ID
+  * "sent" --> sentence text as string
+  * "section" --> publication section the sentence is in
+  * "ner" --> nested list of annotations; each sublist contains the following items:
+              start character position, end character position, annotation text,
+              entity type
+
+Here is an example of a sentence and its annotations:
+```json
+{"PMC4850273": {"annotations":
+                [{"sid": 0,
+                  "sent": "Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont",
+                  "section": "TITLE",
+                  "ner": [
+                    [24,34,"Xyloglucan","chemical"],
+                    [62,67,"Human","species"],]
+                 },]
+}}
+```