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<!DOCTYPE html>
<html>
<title>DEBBIE Project</title>
<meta charset="UTF-8">
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border: 1px solid black;
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</style>
<body>
<!-- Navbar (sit on top) -->
<div class="top">
<div class="w3-bar w3-white w3-wide w3-padding w3-card">
<img src="images/flyer.png" width="60" height="60"></a>
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<div class="w3-right">
<a href="https://projectdebbie.github.io/#about" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">About</a>
<a href="https://projectdebbie.github.io/#ontology" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Ontology</a>
<a href="https://projectdebbie.github.io/#database" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Database</a>
<a href="https://projectdebbie.github.io/documentation.html" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Documentation</a>
<a href="https://projectdebbie.github.io/#research" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Research</a>
<a href="https://projectdebbie.github.io/#team" class="w3-bar-item w3-button w3-padding-16" style="text-decoration:none">Team</a>
<a href="https://projectdebbie.github.io/contact.html" class="w3-bar-item w3-button w3-padding-16">Contact</a>
</div>
</div>
</div>
<br>
<!-- Header -->
<header class="w3-display-container w3-content w3-wide w3-center" style="max-width:1245px; min-width:1245px;" id="home">
<img class="w3-image w3-center" style="border-radius: 25px;" src="images/Debbie_long.png" alt="Debbie_img">
</header>
<!-- Page content max-width:1564px -->
<div class="w3-content w3-padding w3-white" style="max-width:1300px; min-width: 1300px;">
<!-- what is the debbie pipeline? Section -->
<div class="w3-container w3-padding-16 w3-white" id="about" >
<h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">What is the DEBBIE pipeline?</h2>
<p>Powered by software container technology (Docker) and a workflow manager (Nextflow), the DEBBIE pipeline <b>automatically and continuously</b> retrieves research abstracts, filters them according to relevance using the DEBBIE_BioBERT model, annotates concepts using the Biomaterials Annotator, and stores the information within a document-oriented database named the Database of Experimental Biomaterials and their Biological Effect (DEBBIE).
</p>
<br>
<center><img class="w3-image w3-center" src="images/debbie_pipeline_biobert.png" alt="Pipeline" width="900" height="450"></center>
<p>As a starting point for the gathering of relevant biomaterials abstracts, the following PubMed search query is executed: <i>((((((((Biomedical and dental materials[MeSH Terms]) OR (Prostheses and implants[MeSH Terms])) OR (Materials testing[MeSH Terms])) OR (Tissue engineering[MeSH Terms])) OR (Tissue scaffolds[MeSH Terms])) OR (Equipment safety[MeSH Terms])) OR (Medical device recalls[MeSH Terms])) OR (Biomaterials)) OR (Cell scaffolds)</i>.
<p>The <b>DEBBIE_BioBERT</b> model performs multiclass classification of abstracts to determine if they are relevant (either clinical or non-clinical studies) or not relevant to the field of biomaterials.
The DEBBIE_BioBERT model was developed using <b>Transformers</b>, which is the state-of-the-art in NLP. We used the pre-trained BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining) model and trained it on our biomaterial abstracts dataset. This technique is known as fine-tuning.
BioBERT is a domain-specific language representation model pre-trained on large-scale biomedical corpora.
</p>
<h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Watch the <a target="_blank" href="https://youtu.be/9ZMeheWFnYA">DEBBIE video</a> to learn more about its capabilities.</h2>
<video width="1000" height="800" controls preload="metadata">
<source src="videos/debbie.mp4" type="video/mp4">
Your browser does not support the video tag.
</video>
</div>
<!-- what are annotations Section -->
<div class="w3-container w3-padding-16 w3-white" id="about" >
<h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">What are annotations?</h2>
<p>Automated text annotation is a Natural Language Processing (NLP) technique that identifies and extracts relevant concepts hidden within large collections of textual data through computational approaches. In DEBBIE, annotations are performed using the <a href="https://github.com/ProjectDebbie/Biomaterials_annotator">Biomaterials Annotator</a>, an instrument combining several open lexical resource and built using the <a href="https://gate.ac.uk/">General Architecture of Text Engineering (GATE)</a> software and the <a href="https://stanfordnlp.github.io/CoreNLP/">Stanford Core Natural Language Processing (CoreNLP)</a> framework. Below is an example of an annotated abstract in GATE, with identified terms labeled with their respective categories.
</p>
<br>
<center><img class="w3-image w3-center" src="images/annotation_example.png" alt="Pipeline" width="900" height="450"></center>
</div>
<!-- quick start Section -->
<div class="w3-container w3-padding-16 w3-white" id="about" >
<h2 class="w3-border-bottom w3-border-light-grey w3-padding-16">Quick Start</h2>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">DEBBIE's User Interface Search</h3>
<p>
<ol class="list" style="padding-left: 100px;">
<li> Enter a single term into the search field on the <a href="http://debbie.bsc.es/search/">DEBBIE homepage</a> and click the Submit Query button in order to begin the search. <br>
Example of search terms: Fibroin, Encapsulation, Bone </li>
<br><li>The search results page contains a quick summary, showing mentions of the term over the years, other commonly associated terms and the study types where your search term has appeared.</li>
<br><li>Below the quick summary, there are optional annotation categories. Select the categories you wish to explore further, and a drop down box will appear with further information, such as associated top terms. </li>
</ol>
</p>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">DEBBIE's RESTful API</h3>
<p>
<ol class="list" style="padding-left: 100px;">
<li>The contents of DEBBIE are programmatically accessible through the RESTful API located at <a href="https://debbie.bsc.es/search/api/v1"><u>http://debbie.bsc.es/search/api/v1</u></a></li>
<br>
<li>Users can submit different searches through the RESTful API: <br><br>
<ul class="list_api" style="padding-left: 50px;">
<li>
Returns the frequency of usage of the term of interest over time, normalized per abstract: <br>
https://debbie.bsc.es/search/api/v1/search/[term]/years<br>
</li><br>
<li>
Returns the thirteen most frequently annotated terms that are associated (co-occur) with the term of interest in different abstracts: <br>
https://debbie.bsc.es/search/api/v1/search/[term]/top_terms<br>
</li><br>
<li>
Returns the thirteen most frequently annotated terms that co-occurs with term of interest within a particular category: <br>
https://debbie.bsc.es/search/api/v1/search/[term]/top_terms/[type]<br>
Category possible values [type]:<br>
Biomaterial -
BiologicallyActiveSubstance -
ManufacturedObject -
ManufacturedObjectComponent -
MedicalApplication -
ManufacturedObjectFeatures -
Structure -
AssociatedBiologicalProcess -
MaterialProcessing - EffectOnBiologicalSystem
Cell - AdverseEffects
Species - ResearchTechnique
Tissue
</li><br>
<li>Returns network that described the relationships between the term of interest as well as the associated terms: <br>
https://debbie.bsc.es/search/api/v1/search/[term]/network<br></li><br>
<li>
Examples with the term "silk":<br>
https://debbie.bsc.es/search/api/v1/search/silk/years<br>
https://debbie.bsc.es/search/api/v1/search/silk/top_terms<br>
https://debbie.bsc.es/search/api/v1/search/silk/top_terms/Biomaterial<br>
https://debbie.bsc.es/search/api/v1/search/silk/network<br>
</li>
</ol>
</p>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">Annotation Categories</h3>
<table class="w3-table w3-bordered w3-border w3-centered w3-striped">
<tr>
<th>Category</th>
<th>Definition</th>
<th>Examples</th>
</tr>
<tr>
<td>Adverse Effects</td>
<td>An unfavorable or unintended disease, sign, or symptom (including an abnormal laboratory finding) that is temporally associated with the use of a medical device or biomaterial</td>
<td><i>Cytotoxicity, Inflammatory reaction, Abscesses</i></td>
</tr>
<tr>
<td>Associated Biological Process</td>
<td>A cellular or biological process that the manufactured object is designed to cause or support, or is measured to affect</td>
<td><i>Adipogenesis, Angiogenesis, Cell attachment</i></td>
</tr>
<tr>
<td>Biomaterial</td>
<td>A non-drug raw material or substance suitable for inclusion in systems which augment or replace the function of bodily tissues or organs</td>
<td><i>Polydioxanone, Polyglycolide, Hydroxyapatite</i></td>
</tr>
<tr>
<td>Biomaterial Types</td>
<td>Classification or nature of biomaterials</td>
<td><i>Polymer, Ceramic, Metal</i></td>
</tr>
<tr>
<td>Biological Active Substance</td>
<td>Substance included in a manufactured object in order to impart a biological activity</td>
<td><i>Collagen, Heparin, RGD</i></td>
</tr>
<tr>
<td>Cell</td>
<td>The reported cell line or primary cell type</td>
<td><i>Fibroblast, Type II Pneumocyte, Osteocyte</i></td>
</tr>
<tr>
<td>Effect on Biological System</td>
<td>The effect associated with manufactured object in a specific test system (cells, tissue or organism)</td>
<td><i>Biocompatibility, Cytocompatibility, Immunomodulatory</i></td>
</tr>
<tr>
<td>Manufactured Object</td>
<td>A physical object created by hand or machine</td>
<td><i>Experimental scaffold, Medical device, Surgical implant</i></td>
</tr>
<tr>
<td>Manufactured Object Component</td>
<td>A part, region or component referred to as a distinct unit, such as a surface or a layer</td>
<td><i>Core, Shell, Coat </i></td>
</tr>
<tr>
<td>Material Processing</td>
<td>A planned process which results in physical changes in a specified input material</td>
<td><i>Biofabrication, Coating, Knitting</i></td>
</tr>
<tr>
<td>Manufactured Object Features</td>
<td>Characteristics inherent or given during processing to a manufactured object or its components</td>
<td><i>Geometry, Mechanical Property, Physical Property</i></td>
</tr>
<tr>
<td>Medical Application, Disease or Condition</td>
<td>Intended use, context, function or outcome of the manufactured object</td>
<td><i>Artificial organs, Encapsulation, Diabetes, Injury</i></td>
</tr>
<tr>
<td>Research Technique</td>
<td>The reported laboratory technique used in an experimental study</td>
<td><i>Scanning electron microscope, High Performance Liquid Chromatography </i></td>
</tr>
<tr>
<td>Species</td>
<td>The species and /or breed used in the study</td>
<td><i>Rat, Rabbit, Mouse</i></td>
</tr>
<tr>
<td>Structure</td>
<td>The configuration, form or texture associated with a manufactured object or its components</td>
<td><i>Fiber, Gel, Mesh</i></td>
</tr>
<tr>
<td>Tissue</td>
<td>A tissue or an organ mentioned in the study as the target or test system for the biomaterial object or medical device</td>
<td><i>Lung epithelium, Nerve plexus, Elastic cartilage tissue</i></td>
</tr>
</table>
<br>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">Ontology/Terminology Sources</h3>
<!-- list of superclasses -->
<ul class="ontology" style="padding-left: 150px;">
<!--row 1 -->
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/MESH">Medical Subject Headings (UMLS)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/DEB">Devices, Experimental Scaffolds and Biomaterials Ontology (DEB)</a></li>
<li class="ontology"><a href="https://www.gmdnagency.org/">Global Medical Device Nomenclature (GMDN)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/CHEBI">Chemical Entities of Biological Interest (CHEBI)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/IOBC">Interlinking Ontology for Biological Concepts (IOBC)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/NCIT">National Cancer Institute Thesaurus (NCIT)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/NPO">NanoParticle Ontology (NPO)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/OBI">Ontology for Biomedical Investigations (OBI)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/ONTOTOXNUC">Ontology of Nuclear Toxicity (ONTOTOXNUC)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/UBERON">Uber Anatomy Ontology (UBERON)</a></li>
<li class="ontology"><a href="https://bioportal.bioontology.org/ontologies/PREMEDONTO">Precision Medicine Ontology (PREMEDONTO)</a></li>
</ul>
<br>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">Individual Pipeline Components and Databases</h3>
<table class="w3-table w3-bordered w3-border w3-centered w3-striped">
<tr>
<th>Name</th>
<th>Availability</th>
<th>Brief Description</th>
</tr>
<tr>
<td>PubMed Retrieval Tool</td>
<td><a href="https://github.com/ProjectDebbie/pubmed_retrieval"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a><a href="https://hub.docker.com/repository/docker/projectdebbie/pubmed_retrieval"><img style="padding-top: 2px;" class="w3-image w3-center" src="images/dockerhub_icon.png" width="30" height="30"></a></td>
<td>Takes a desired time frame and retreives PMID, title, abstract, and publication date (month and year) of all records archived by PubMed over that period.</td>
</tr>
<tr>
<td>PubMed Standardization Tool</td>
<td><a href="https://github.com/ProjectDebbie/pubmed_retrieval"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a><a href="https://hub.docker.com/repository/docker/projectdebbie/pubmed_standardization"><img style="padding-top: 2px;" class="w3-image w3-center" src="images/dockerhub_icon.png" width="30" height="30"></a></td>
<td>Takes a PubMed abstract collection in XML format stored in a working directory and standardizes the content, generating an individual plain text file for each abstract.</td>
</tr>
<tr>
<td>Gold Standard Literature Set</td>
<td><a href="https://github.com/ProjectDebbie/pubmed_retrieval"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>The gold standard set is a list of PMIDs for abstracts selected to represent the biomaterials literature, with focus on biological evaluation of biomaterials and biocompatibility.</td>
</tr>
<tr>
<td>Background Literature Set</td>
<td><a href="https://github.com/ProjectDebbie/background_set"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>The backgroud set is a list of PMIDs representing non-biomaterials abstracts for the purpose of relevance classification.</td>
</tr>
<tr>
<td>Classifier</td>
<td><a href="https://github.com/ProjectDebbie/Classifier"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a><a href="https://hub.docker.com/repository/docker/projectdebbie/classifier"><img style="padding-top: 2px;" class="w3-image w3-center" src="images/dockerhub_icon.png" width="30" height="30"></a></td>
<td>This component performs binary classification of abstracts to determine if they are relevant or not relevant to the field of biomaterials.</td>
</tr>
<tr>
<td>OWL2DICT Tool</td>
<td><a href="https://github.com/ProjectDebbie/owl_to_dict"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>Maps out the entire OWL file to retrieve all child classes found within the selected categories as terms, each term’s class memberships, as well as any associated synonyms and properties.</td>
</tr>
<tr>
<td>OWL2DICT-lite Tool</td>
<td><a href="https://github.com/ProjectDebbie/owl_to_dict/blob/master/owl2dict_light.py"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>A simpler implementation of owlready2. It retrieves all classes (but no properties) for given ancestors from an .owl ontology provided locally.</td>
</tr>
<tr>
<td>Biomaterial Annotator</td>
<td><a href="https://github.com/ProjectDebbie/Biomaterials_annotator"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a><a href="https://hub.docker.com/repository/docker/projectdebbie/biomaterials-annotator"><img style="padding-top: 2px;" class="w3-image w3-center" src="images/dockerhub_icon.png" width="30" height="30"></a></td>
<td>The biomaterials annotator is a lexical resource for performing annotations on the biomaterials literature</td>
</tr>
<tr>
<td>GATE-TO-JSON Tool</td>
<td><a href="https://github.com/ProjectDebbie/gate_to_json"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a><a href="https://hub.docker.com/repository/docker/projectdebbie/gate_to_json"><img style="padding-top: 2px;" class="w3-image w3-center" src="images/dockerhub_icon.png" width="30" height="30"></a></td>
<td>This component exports debbie annotations in XML GATE format to JSON format.</td>
</tr>
<tr>
<td>Import JSON-TO-MONGO Tool</td>
<td><a href="https://gitlab.bsc.es/inb/text-mining/generic-tools/import-json-to-mongo"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>This component inserts and pushes JSON files into a designated MongoDB.</td>
</tr>
<tr>
<td>Complete Pipeline Tool</td>
<td><a href="https://github.com/ProjectDebbie/DEBBIE_pipeline"><img style="opacity: 0.5" class="w3-image w3-center" src="images/github_icon.png" width="30" height="30"></a></td>
<td>The automated pipeline retrieves biomaterials abstracts from PubMed, annotates them using multiple lexical assets, and deposits the annotated abstracts in a MongoDB.</td>
</tr>
<!-- <tr>
<td>DEBBIE User Interface</td>
<td></td>
<td>This repository contains the individual HTML templates, the Python Flask application, and the REST API application.</td>
</tr> -->
</table>
<br>
<h3 class="w3-border-bottom w3-border-light-grey w3-padding-16">Citing DEBBIE</h3>
<p>
Corvi, J. O., McKitrick, A., Fernández, J. M., Fuenteslópez, C. V., Gelpí, J. L., Ginebra, M. P., Capella-Gutierrez, S., & Hakimi, O. (2023). DEBBIE: The Open Access Database of Experimental Scaffolds and Biomaterials Built Using an Automated Text Mining Pipeline. Advanced healthcare materials, 12(25), e2300150. https://doi.org/10.1002/adhm.202300150
</p>
<p>
Corvi, J., Fuenteslópez, C., Fernández, J., Gelpi, J., Ginebra, M.-P., Capella-Guitierrez, S., Hakimi, O. The biomaterials annotator: a systemfor ontology-based concept annotation of biomaterials text. In:Proceedings of the Second Workshop on Scholarly DocumentProcessing, pp. 36–48. Association for Computational Linguistics,Online (2021). https://www.aclweb.org/anthology/2021.sdp-1.5
</p>
<p>Hakimi, O., Gelpi, J., Krallinger, M., Curi, F., Repchevsky, D., Ginebra, M.-P. The devices, experimental scaffolds, and biomaterials ontology (deb): A tool for mapping,
annotation, and analysis of biomaterials’ data. Adv. Funct. Mater. (2020)
</p>
</div>
<!-- Funding Section -->
<div class='container'>
<div class='image-container' style="max-width:2000px;">
<img style= "float: left; border-radius: 25px; width:10%; height:10%;" src="images/eu_flag.png" alt="eu_flag">
<p style = "margin-left: 150px; padding-top: 20px"> This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 751277.</p>
</div>
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