diff --git a/.github/workflows/extract.yml b/.github/workflows/extract.yml index 5a391ca..ee8aae9 100644 --- a/.github/workflows/extract.yml +++ b/.github/workflows/extract.yml @@ -19,8 +19,21 @@ jobs: with: java-version: 17 distribution: 'temurin' + - name: Cache Groovy/Maven dependencies + uses: actions/cache@v4 + with: + path: | + ~/.groovy/grapes + ~/.groovy/grapeCache + ~/.ivy2/cache + ~/.m2/repository + key: ${{ runner.os }}-grapes-${{ hashFiles('extractOWL.groovy') }} + restore-keys: | + ${{ runner.os }}-grapes- - name: Install dependencies - run: sudo apt install groovy + run: sudo apt-get update && sudo apt-get install -y groovy pandoc + - name: Generate temporary HTML from index.md + run: pandoc index.md -s -o index.html - name: Extract OWL run: groovy extractOWL.groovy | tee glossary.owl - name: Commit OWL file diff --git a/extractOWL.groovy b/extractOWL.groovy index b031605..75208b6 100644 --- a/extractOWL.groovy +++ b/extractOWL.groovy @@ -6,6 +6,7 @@ import org.apache.any23.Any23 import org.apache.any23.source.HTTPDocumentSource +import org.apache.any23.source.FileDocumentSource import org.apache.any23.writer.NTriplesWriter workspaceRoot = "../ws" @@ -16,7 +17,15 @@ url = "https://vhp4safety.github.io/glossary/" Any23 runner = new Any23(); runner.setHTTPUserAgent("test-user-agent"); httpClient = runner.getHTTPClient() -source = new HTTPDocumentSource(runner.getHTTPClient(), url) +// prefer a local file if provided as an argument or if index.html exists +source = null +if (this.args?.length && new File(this.args[0]).exists()) { + source = new FileDocumentSource(new File(this.args[0])) +} else if (new File('index.html').exists()) { + source = new FileDocumentSource(new File('index.html')) +} else { + source = new HTTPDocumentSource(runner.getHTTPClient(), url) +} out = new ByteArrayOutputStream(); handler = new NTriplesWriter(out); @@ -33,6 +42,7 @@ rdf.addPrefix(kb, "skos", "http://www.w3.org/2004/02/skos/core#") rdf.addPrefix(kb, "dc", "http://purl.org/dc/elements/1.1/") rdf.addPrefix(kb, "dct", "http://purl.org/dc/terms/") rdf.addPrefix(kb, "ncit", "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#") +rdf.addPrefix(kb, "chebi", "http://purl.obolibrary.org/obo/chebi/") rdf.addPrefix(kb, "og", "http://ogp.me/ns#") rdf.importFromStream(kb, n3Stream, "N3") diff --git a/glossary.owl b/glossary.owl index ed452d9..e69de29 100644 --- a/glossary.owl +++ b/glossary.owl @@ -1,1195 +0,0 @@ -@prefix biopax: . -@prefix dc: . -@prefix dct: . -@prefix gpml: . -@prefix ncit: . -@prefix og: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix wp: . -@prefix xsd: . - - - rdf:type owl:Class ; - rdfs:label "Prompt"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "An input provided to a model to guide its output or action. Prompts can take various forms, such as text, images, audio, or structured data, depending on the capabilities of the model."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Human-Readable Data"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A data or dataset that is in a format that can be naturally read by humans. It usually contrasts with machine-readable data. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Silibinin"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "mixture "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Data steward"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A data steward is an oversight or data governance role within an organization, and is responsible for ensuring the quality and fitness for purpose of the organization's data assets, including the metadata for those data assets. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Physiologically based kinetic model"@en-US ; - ncit:C42610 "PBK model"@en-US ; - dc:description "See PBPK model (these terms are equivalent)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Application Programming Interface"@en-US ; - ncit:C42610 "API"@en-US ; - dc:description "A type of software interface that provides a way for two or more computer programs to communicate with each other. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "European Chemical Agency"@en-US ; - ncit:C42610 "ECHA"@en-US ; - dc:description "An agency of the European Union which manages the technical and administrative aspects of the implementation of the European Union regulation called Registration, Evaluation, Authorisation and Restriction of Chemicals. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "nan"@en-US ; - ncit:C42610 ""@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "xanthohumol"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey ORXQGKIUCDPEAJ-YRNVUSSQSA-N, CAS registry number 6754-58-1 "@en-US . - -[ rdf:type ; - - "Webpage with the VHP4Safety Glossary" ; - "VHP4Safety Glossary" ; - "glossary" ; - -] . - - - rdf:type owl:Class ; - rdfs:label "Mn²⁺"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey WAEMQWOKJMHJLA-UHFFFAOYSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "User experience"@en-US ; - ncit:C42610 "UX"@en-US ; - dc:description "The experience a user would go through when interacting with a company, its services, and its products. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Sprint"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A fixed time-box, usually 1-4 weeks, used in the SCRUM method of working. Per sprint, each team member works on selected tasks which they can (likely) finish within the sprint. Each sprint has meetings to plan the sprint, review the finished tasks and reflect to improve productivity."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Mathematical Markup Language"@en-US ; - ncit:C42610 "MathML"@en-US ; - dc:description "An Extensible Markup Language (XML) application to encode mathematical notations on the Web to capture their structure and content for their use and re-use. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 1.3"@en-US ; - ncit:C42610 "WP1.3"@en-US ; - dc:description "Computational toxicodynamics: objectives to develop QSAR and MIE prediction models, develop qAOPs, testing the platform and generating safety estimates."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Metadata"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The data that provide information about one or more aspects of the data that is used to summarize basic information about data that can make tracking and working with specific data easier."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Stressor"@en-US ; - ncit:C42610 ""@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "Lowest Observed Adverse Effect Level"@en-US ; - ncit:C42610 "LOAEL"@en-US ; - dc:description "The lowest exposure level of a chemical stressor evaluated in a toxicity test that shows harmful effects on a plant or animal."@en-US . - - - rdf:type owl:Class ; - rdfs:label "General Tools"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Support software tools that can be used at several stages of a workflow."@en-US . - - - rdf:type owl:Class ; - rdfs:label "User Story"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A simple, clear description of a desired feature or functionality from the perspective of the end user. Typically follows the format: 'As as [user], I want [feature], so that [benefit].'. Each task in the backlog should be contributing to as user story, each user story should be contributing to an epic."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Module"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "[Software Component]An individual component (software, dataset or in vitro method description) that is hosted, or linked to in the VHP4Safety platform. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Platform"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A computer environment where a set of software and tools are hosted and made available for the use of others over the internet. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 4"@en-US ; - ncit:C42610 "WP4"@en-US ; - dc:description "Project Coordination, Impact and Data Management: objectives to ensure that project objectives are achieved, deliverables are completed, manage overall knowledge utilisation, and provide effective and sustainable data management."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Pharmacokinetics"@en-US ; - ncit:C42610 "PK"@en-US ; - dc:description "see ADME (these terms are equivalent)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Kubernetes"@en-US ; - ncit:C42610 "K8s"@en-US ; - dc:description "A computer tool to orchesterize and manage Docker containers."@en-US . - - - rdf:type owl:Class ; - rdfs:label "No Observed Effect Level"@en-US ; - ncit:C42610 "NOEL"@en-US ; - dc:description "The highest exposure level of a chemical stressor evaluated in a toxicity test that shows no effects on a plant or animal."@en-US . - - - rdf:type owl:Ontology ; - dct:contributor "Egon Willighagen"@en-US , "Javier Millán Acosta"@en-US , "Marvin Martens"@en-US , "Ozan Çınar"@en-US ; - dct:title "VHP4Safety Glossary"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Internal (Exposure)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The amount of a chemical (or its active metabolites) present in human tissues or biological fluids over time, typically expressed as concentration-time profiles or dose metrics, resulting from external exposure after ADME/TK processes, and used as the input for the Toxicodynamics/AOP step."@en-US . - - - rdf:type owl:Class ; - rdfs:label "NH-3"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "chemical compound, InChIKey IXMROOKFPWGDGF-UHFFFAOYSA-N, CAS registry number 447415-26-1 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "endosulfan"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "mixture, InChIKey RDYMFSUJUZBWLH-AZVNHNRSSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Token"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The basic unit of text processed by a language model, which can be a word, part of a word, or even a single character, depending on the model’s tokenizer."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Large Language Model"@en-US ; - ncit:C42610 "LLM"@en-US ; - dc:description "A large language model is a computational model capable of language generation or other natural language processing tasks. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Task Force"@en-US ; - ncit:C42610 "TF"@en-US ; - dc:description "Cross work package effort to reach some goal."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Research Line 1"@en-US ; - ncit:C42610 "RL1"@en-US ; - dc:description "Building the Virtual Human Platform."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Findable, Accessible, Interoperable, Reusable"@en-US ; - ncit:C42610 "FAIR"@en-US ; - dc:description "The FAIR principles emphasise machine-actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in volume, complexity, and creation speed of data. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Adverse Outcome Pathway"@en-US ; - ncit:C42610 "AOP"@en-US ; - dc:description "An AOP describes a sequence of events commencing with initial interaction(s) of a stressor with a biomolecule within an organism that causes a perturbation in its biology (i.e., molecular initiating event, MIE), which can progress through a dependent series of intermediate key events (KEs) and culminate in an adverse outcome (AO) considered relevant to risk assessment or regulatory decision-making. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Benchmark dose"@en-US ; - ncit:C42610 "BMD"@en-US ; - dc:description "See Benchmark dose modeling"@en-US . - - - rdf:type owl:Class ; - rdfs:label "amiodarone hydrochloride"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey ITPDYQOUSLNIHG-UHFFFAOYSA-N, CAS registry number 19774-82-4 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Interability"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The ability to explain or to present a model, such as Large Language Models and machine learning systems in understandable terms to a human. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Product Owner"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A key role in SCRUM method for people who have a clear view of the long term goals of the project and the expertise of the team members. People with this role review the epics and user stories and prioritize the tasks in the backlog."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Hazard Assessment"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The process of assessing the intrinsic hazard a substance poses to human health and/or the environment. This provides information on potential human health effects such that a safe production and use of a chemical can be assured. Two types can be generally distinguished, i.e. with the purpose to classify the chemical to a certain category of toxicity (mostly qualitative assessment) or to derive an exposure limit, such as a health-based guidance value or product limit, that ensures safe use."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Scalability"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The property of a (cloud) infrastructure to be able to handle a growing amount of data and work related to it with additions. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 2.3"@en-US ; - ncit:C42610 "WP2.3"@en-US ; - dc:description "Life course exposure - Case study neurodegenerative disease and life course exposure to chemicals: objectives to identify critical physiological pathways, model life time exposure, develop AOP networks, test toxicity and assess the safety of selected chemicals."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Ontology"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A formal specification of the conceptualization of a set of phenomena naming and defining the elements of the set along with describing relations between the concepts, data, and entities; a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Quantitative Adverse Outcome Pathway"@en-US ; - ncit:C42610 "qAOP"@en-US ; - dc:description "Quantitative AOPs, \"Leiden approach\" to connect events using differential equations."@en-US . - - - rdf:type owl:Class ; - rdfs:label "New Approach Methodology"@en-US ; - ncit:C42610 "NAM"@en-US ; - dc:description "A collection of various methods (e.g., high-throughput screening and high-content methods) in a wide set of contexts including in chemico and in vitro to improve knowledge over the toxicokinetic or toxicodynamic attributes of chemical substances, and in turn to improve the chemical safety assessment (see also Non-Animal Methodology). "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Process Flow Step"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "One of the generic stages in the VHP4Safety human-based risk-assessment workflow, used to structure tools, data and models along the risk assessment process."@en-US . - - - rdf:type owl:Class ; - rdfs:label "chlorpyrifos"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey SBPBAQFWLVIOKP-UHFFFAOYSA-N, CAS registry number 2921-88-2 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Standardization"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process of developing, implementing, and maintaining technical standards to ensure consistency, uniformity, and compatibility across products, processes, or services."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Non-Animal Methodology"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A collection of methods to evaluate the potential for a chemical to cause systematic toxicity without using tests on animals (see also New Approach Methodology). "@en-US . - - - rdf:type owl:Class ; - rdfs:label "nan"@en-US ; - ncit:C42610 "ZIN"@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "Physiologically based toxicokinetic model"@en-US ; - ncit:C42610 "PBTK"@en-US ; - dc:description "See PBPK model (these terms are equivalent)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "VHP server 1"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The server provided by Strato where the Docker containers used in the project are deployed."@en-US . - - - rdf:type owl:Class ; - rdfs:label "T4"@en-US ; - ncit:C42610 "T4"@en-US ; - dc:description "type of a chemical entity, InChIKey XUIIKFGFIJCVMT-LBPRGKRZSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Mode of Action"@en-US ; - ncit:C42610 "MoA"@en-US ; - dc:description "A functional or anatomical change, resulting from the exposure of a living organism to a substance."@en-US . - - - rdf:type owl:Class ; - rdfs:label "cefuroxime"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey JFPVXVDWJQMJEE-IZRZKJBUSA-N, CAS registry number 55268-75-2 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Retrieval-Augmented Generation"@en-US ; - ncit:C42610 "RAG"@en-US ; - dc:description "A technique that combines retrieval systems (e.g., search engines or databases) with generation models like LLMs. The retrieval system provides relevant context or data, which the generation model then uses to create accurate and context-aware responses."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Natural Language Processing"@en-US ; - ncit:C42610 "NLP"@en-US ; - dc:description "A multidisciplinary scientific field that focuses on the interaction between computers and human (natural) languages, enabling machines to understand, interpret, and generate human language in a meaningful way. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Bioactivity"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The affinity and/or potency of a compound for a protein target."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 1.1"@en-US ; - ncit:C42610 "WP1.1"@en-US ; - dc:description "Building the ICT infrastructure for the VHP: objectives to develop the technical infrastructure, setting up a predictive platform, developing analysis workflows, making services and data available and interoperable."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Interoperable"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "To speed up discovery and uncover new insights, research data should be easily combined with other datasets, applications and workflows by humans as well as computer systems. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Key Event"@en-US ; - ncit:C42610 "KE"@en-US ; - dc:description "A change in biological or physiological state that is both measurable and essential to the progression of a defined biological perturbation leading to a specific adverse outcome. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Developmental Neurotoxicity"@en-US ; - ncit:C42610 "DNT"@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "Exposure"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Contact between a toxicological agent and an outer boundary of an organism."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Sprint Review"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A meeting at the end of a sprint where the team presents their work and discuss any issues. The goal is to review the completed tasks and adapt the backlog accordingly. This meeting can be combined with the Sprint Retrospective."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Hackathon"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "An event in which computer programmers collaborate intensively with one another and sometimes with people in other specialties over a relatively short period of time to create code usually for a new software product or service. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Widget"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A small software application that is designed to provide a specific piece of information (such as news, weather, or traffic updates) or a specific function (such as taking notes or controlling another application) on demand. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 3.2"@en-US ; - ncit:C42610 "WP3.2"@en-US ; - dc:description "Acceptance of VHP for safety assessment: objectives to position the VHP in the transition to animal-free safety assessment, raise awareness, investigate uncertainties and acceptance of safety assessments."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Model"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A simplified (generally mathematical) representation of a real system (e.g. of system: an organism, an organ, a cell, etc.)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Docker container"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The virtual environment that has been initiated to run based on its Docker image."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Read accross"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A common approach in the risk assessment in order to examine structural similarities between the source and the target substances when there is a lack of information on their physical-chemical, toxicological properties, or environmental fate."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Toxicokinetics/ADME (Process Flow Step)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process flow step that is named after toxicokinetics and categorizes services that analyze the kinetics (absorption, distribution, metabolism and excretion) of chemicals and how these processes influence the internal dose. The kinetics step contains four physiological processes substeps: Absorption, Distribution, Metabolism, and Excretion which can be captured in PBK models."@en-US ; - dct:relation . - - - rdf:type owl:Class ; - rdfs:label "lesinurad"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "chemical compound, InChIKey FGQFOYHRJSUHMR-UHFFFAOYSA-N, CAS registry number 878672-00-5 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "(R)-dinoseb"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey OWZPCEFYPSAJFR-ZCFIWIBFSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Agent"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A software entity that uses a language model to autonomously perform specific tasks by interpreting prompts, interacting with data or systems, and generating results."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Stakeholder"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A person or a group of people who hold(s) a stake and/or can influence decision-making on a specific issue."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Web Ontology Language"@en-US ; - ncit:C42610 "OWL"@en-US ; - dc:description "RDF standard for making ontologies machine readable."@en-US . - - - rdf:type owl:Class ; - rdfs:label "In vitro in vivo extrapolation"@en-US ; - ncit:C42610 "IVIVE"@en-US ; - dc:description "A method to conduct the qualitative or quantitative transposition of experimental results or observations made in vitro to predict phenomena in vivo, biological organisms. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Data stewardship"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The work performed by a data steward."@en-US . - - - rdf:type owl:Class ; - rdfs:label "European Food Safety Authority"@en-US ; - ncit:C42610 "EFSA"@en-US ; - dc:description "Legislator"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Zn²⁺"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey PTFCDOFLOPIGGS-UHFFFAOYSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Atomic Site of Metabolism"@en-US ; - ncit:C42610 "SOM"@en-US ; - dc:description "The atomic site in a molecule which is prone to metabolism by Cytochrome P450s (or other enzymes) as referred in the SOM Prediction tool."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Backlog"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A prioritized list of all the tasks the team still wants to complete, used in the SCRUM method of working. Each added task is clearly described and preferably linked to an epic and a user story. At the beginning of a sprint, tasks will be selected from the backlog and assigned to team member to be completed before the end of that sprint."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Data modeling"@en-US ; - ncit:C42610 "DMP"@en-US ; - dc:description "The process of discovering, analyzing, and scoping data requirements, and then representing and communicating these data requirements in a precise form called the data model. This process is iterative and may include a conceptual, logical, and physical model. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Workflow"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "An orchestrated and repeatable multi-step process to coordinate multiple tasks and their data dependencies. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 2.1"@en-US ; - ncit:C42610 "WP2.1"@en-US ; - dc:description "In vitro models to provide toxicokinetics & toxicodynamics parameters: objectives to verify in vitro models for ADME and local toxicity, obtaining parameters for PBK modelling, test chemicals on iPSC models."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Open Data"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A (collection of) data that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions only to ensure that further recipients can also do these things. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Molecular Adverse Outcome Pathways"@en-US ; - ncit:C42610 "mAOP"@en-US ; - dc:description "Metapathway, similar to conventional AOPs, but connected events as e.g. WikiPathways pathways. Their function is to expand KEs with molecular pathways and allow analyses of omics data."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Monte Carlo Risk Assessment"@en-US ; - ncit:C42610 "MCRA"@en-US ; - dc:description "See Monte Carlo Risk Assessment calculation model."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Case Study"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A human-health scenario used as a guiding use case within the VHP4Safety Project to integrate data, models, and tools, and to formulate specific regulatory questions that the Virtual Human Platform should be able to answer."@en-US . - - - rdf:type owl:Class ; - rdfs:label "tetrabromobisphenol A"@en-US ; - ncit:C42610 "TBBPA"@en-US ; - dc:description "bisphenol, InChIKey VEORPZCZECFIRK-UHFFFAOYSA-N, CAS registry number 79-94-7 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Epic"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A long-term goal or general feature of the final product. Epics are broken down into user stories, whereas user stories are broken down into tasks. By completing tasks in each sprint, the epic will gradually be reached."@en-US . - - - rdf:type owl:Class ; - rdfs:label "induced Embryonic Stem Cell"@en-US ; - ncit:C42610 "iPSCs"@en-US ; - dc:description "A type of pluripotent stem cell that can be generated directly from adult cells. The process of creating iPSCs involves reprogramming differentiated somatic cells (such as skin or blood cells) by introducing specific genes that reset the cells to a pluripotent state. This reprogramming allows iPSCs to develop into almost any cell type in the body, similarly to hESCs, making them highly valuable for regenerative medicine, disease modelling, and drug discovery."@en-US . - - - rdf:type owl:Class ; - rdfs:label "European Medicines Agency"@en-US ; - ncit:C42610 "EMA"@en-US ; - dc:description "An agency of the European Union (EU) in charge of the evaluation and supervision of pharmaceutical products. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Toxicokinetics"@en-US ; - ncit:C42610 "TK"@en-US ; - dc:description "see ADME (these terms are equivalent, although TK is used exclusively for toxic substances)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Secure Shell"@en-US ; - ncit:C42610 "ssh"@en-US ; - dc:description "A network protocol to access a network service remotely and securely."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Apical Endpoint"@en-US ; - ncit:C42610 ""@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "Adverse Outcome (Process Flow Step)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process flow step that is named after adverse outcome, although specifically refers to clinical and epidemiological effects. It categorizes services that provide information on the toxicological endpoints and adverse outcomes at a clinical or epidemiological level of chemical exposures."@en-US ; - dct:relation . - - - rdf:type owl:Class ; - rdfs:label "β-endosulfan"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey RDYMFSUJUZBWLH-LLXUDWAZSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Prompt Engineering"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The process of designing and refining prompts to achieve desired outputs from a model, often used to maximize performance in specific tasks."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Adapter"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A framework to fine-tune (large language) models by adding a small number of external parameters without the need of the entire (large language) model. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package"@en-US ; - ncit:C42610 "WP"@en-US ; - dc:description "Formal structure within a project to reach some goal."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Research Line 2"@en-US ; - ncit:C42610 "RL2"@en-US ; - dc:description "Feeding the Virtual Human Platform."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Findable"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Metadata and data should be easy to find for both humans and computers. Machine-readable metadata are essential for automatic discovery of datasets and services. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Molecular Initiating Event"@en-US ; - ncit:C42610 "MIE"@en-US ; - dc:description "A specialised type of key event that represents the initial point of chemical/stressor interaction at the molecular level within the organism that results in a perturbation that starts the AOP. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Benchmark dose modeling"@en-US ; - ncit:C42610 "BMD"@en-US ; - dc:description "An approach to determine the toxicological limit values for human health, such as the acceptable daily intake (ADI), of all chemical substances (e.g., food) regardless of type or origin. BMD modeling (possibly in combination with PBK modeling) analyzes in conjunction with multiple test systems and organ systems, to study how exposure variation has on the outcome of an in vitro test system."@en-US . - - - rdf:type owl:Class ; - rdfs:label "PBDE-99"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey WHPVYXDFIXRKLN-UHFFFAOYSA-N, CAS registry number 60348-60-9 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Compound Wiki ID"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Identifier used by the VHP4Safety Compound Wiki (see compoundcloud.wikibase.cloud/wiki/Item:Q1 where Q1 is the Compound Wiki ID for aflatoxin B1)."@en-US . - - - rdf:type owl:Class ; - rdfs:label "SCRUM Board"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The documentation of the tasks in the backlog, tasks in the current sprint, the user stories, the epics and the completed tasks when working in SCRUM. Usually shared and edited through GitHub Projects, Notion or similar tools."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Safety Assessment"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The overarching term for hazard and risk assessment in toxicology. For pharmaceuticals, this term is generally used for assessments of the safety of a certain application of pharmaceuticals, including the determination of the therapeutic window and risk/benefit analysis."@en-US . - - - rdf:type owl:Class ; - rdfs:label "VHP server 3"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The server provided by Strato that is used for experimentation, learning, and testing the work that is carried out on VHP servers 1 and 2."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 2.4"@en-US ; - ncit:C42610 "WP2.4"@en-US ; - dc:description "Age and gender specific safety - Case study Thyroid mediated developmental neurotoxicity: objectives to collect mechanistic physiological data, determine critical pathways, establish quantitative AOP network, identify gender-specific sentitivities and compounds that discriminate, and assess the safety of compound exposure."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Sysrev"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Ortec's literature reviewer support and curation documentationn storage system."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Docker"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A service to create a virtual computer environment which can include the required software/tools to conduct a scientific work."@en-US . - - - rdf:type owl:Class ; - rdfs:label "High Throughput Screening"@en-US ; - ncit:C42610 "HTS"@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "sulfobromophthalein"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey OHTXTCNTQJFRIG-UHFFFAOYSA-N, CAS registry number 297-83-6 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Hazard/Chemical Characteristics (Process Flow Step)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process flow step that is named after hazard assessment and considered to be cheminformatics-based. It categorizes services that use molecular structures, chemical descriptors, and databases to predict or analyze the properties, behavior, and potential risks of chemical substances."@en-US ; - dct:relation . - - - rdf:type owl:Class ; - rdfs:label "dinoseb"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "mixture "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Blood Brain Barrier"@en-US ; - ncit:C42610 "BBB"@en-US ; - dc:description "A tissue to protect the brain and spinal cord from both toxic and pathogenic agents in the blood. It is formed by extensive tight junctions between vascular epithelial cells, which are polarized into luminal (blood-facing) and abluminal (brain-facing) plasma membrane domains."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Machine-Readable Data"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A data or dataset that is in a format that can be read by a computer. It usually contrasts with human-readable data. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "silymarin"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "extract "@en-US , "mixture "@en-US . - - - rdf:type owl:Class ; - rdfs:label "College voor de toelating van gewasbeschermingsmiddelen en biociden"@en-US ; - ncit:C42610 "CTBG"@en-US ; - dc:description "Dutch Board for the Authorisation of Plant Protection Products and Biocides. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Physiologically based biokinetic model"@en-US ; - ncit:C42610 "PBBK"@en-US ; - dc:description "See PBPK model (these terms are equivalent)"@en-US . - - - rdf:type owl:Class ; - rdfs:label "VHP server 2"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The server provided by Strato where the Kubernetes structure is formed for orchestration of the Docker containers on VHP server 1."@en-US . - - - rdf:type owl:Class ; - rdfs:label "T3"@en-US ; - ncit:C42610 "T3"@en-US ; - dc:description "type of a chemical entity, InChIKey AUYYCJSJGJYCDS-LBPRGKRZSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "European Centre for the Validation of Alternative Methods"@en-US ; - ncit:C42610 "ECVAM"@en-US ; - dc:description "The EU Reference Laboratory for alternatives to animal testing, located in Ispra, Italy."@en-US . - - - rdf:type owl:Class ; - rdfs:label "monobutyl phthalate"@en-US ; - ncit:C42610 "MBP"@en-US ; - dc:description "type of a chemical entity, InChIKey YZBOVSFWWNVKRJ-UHFFFAOYSA-N, CAS registry number 131-70-4 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "ethylenebis(dithiocarbamate)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey AWYFNIZYMPNGAI-UHFFFAOYSA-L "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Explainability"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The ability to describe the internal logic and mechanics of a model, such as Large Language Models and machine learning systems, to understand the way the model is trained and how predictions and answers are generated by the model. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "SCRUM"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "An agile way of working as a development team that uses time-boxed iterations called sprints to focus on fully executing smaller increments of a larger product. It includes clear bite-sized tasks, regular discussions and collaborative review. It tackles issues such as vague long term goals, poor teamwork and inefficient timespending."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Proteochemometric"@en-US ; - ncit:C42610 "PCM"@en-US ; - dc:description "Mathematical models that can be used to predict the biological properties (mainly bioactivity) of compounds on proteins from the knowledge of their (chemical) structure."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 1.2"@en-US ; - ncit:C42610 "WP1.2"@en-US ; - dc:description "In silico toxicokinetics: objectives to define parameters required for PBPK modelling, developing PBK models and providing guidance for in vitro to in vivo extrapolations."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Reusable"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Research data should be ready for future research and future processing, making it self-evident that findings can be replicated and that new research effectively builds on already acquired, previous results. "@en-US . - -[ rdf:type ; - - "Webpage with the VHP4Safety Glossary" ; - "VHP4Safety Glossary" ; - "glossary" ; - -] . - - - rdf:type owl:Class ; - rdfs:label "Key Event Relationship"@en-US ; - ncit:C42610 "KER"@en-US ; - dc:description "A scientifically-based relationship that connects one key event to another, defines a causal and predictive relationship between the upstream and downstream event, and thereby facilitates inference or extrapolation of the state of the downstream key event from the known, measured, or predicted state of the upstream key event. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "(human) Embryonic Stem Cell"@en-US ; - ncit:C42610 "(h)ESCs"@en-US ; - dc:description "Pluripotent stem cells derived from the inner cell mass of a blastocyst (an early-stage pre-implantation embryo). These cells are characterised by their ability to differentiate into any cell type of the three germ layers: ectoderm, mesoderm, and endoderm. They are also known for their self-renewal capability, meaning they can proliferate indefinitely in culture while maintaining their pluripotency."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Chemical Information Tool"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Software used to transform and process chemical information items."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Sprint Retrospective"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A meeting after the Sprint Review where the team reflects on the process of sprint that was reviewed. It focuses on the aspects of the last sprint that went well or bad, and how the team can improve their work in the next sprint."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Research Output Management Plan"@en-US ; - ncit:C42610 "ROMP"@en-US ; - dc:description "Descriprion of the process of organising and documenting the diverse range of outputs generated during the research lifecycle. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "rotenone"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "chemical compound, InChIKey JUVIOZPCNVVQFO-HBGVWJBISA-N, CAS registry number 83-79-4 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Catalog"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A systemic collection of items of the same type. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 3.3"@en-US ; - ncit:C42610 "WP3.3"@en-US ; - dc:description "Training and Education: objectives to promote collaboration, facilitate transferability of methods and models, implementing new teaching modules, promote capacity building and awareness of stakeholders, improve skills regarding risk communication."@en-US . - - - rdf:type owl:Class ; - rdfs:label "amiodarone"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "chemical compound, InChIKey IYIKLHRQXLHMJQ-UHFFFAOYSA-N, CAS registry number 1951-25-3 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Absorption, Distribution, Metabolism, and Excretion"@en-US ; - ncit:C42610 "ADME"@en-US ; - dc:description "Absorption, distribution, metabolism, and excretion of a substance (toxic or not) in a living organism, following exposure to this substance"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Docker image"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A representative file from which a docker container can be run and executed."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Teratology"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "Scientific field that studies the causes, mechanisms, and classes of congenital malformations in animals and plants. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Toxicodynamics/AOP (Process Flow Step)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process flow step that is named after Toxicodynamics and categorizes services that use or extend the (quantitative) AOP framework to analyze and assess the interaction of chemicals with biological targets."@en-US ; - dct:relation . - - - rdf:type owl:Class ; - rdfs:label "silychristin A"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "chemical compound, InChIKey BMLIIPOXVWESJG-LMBCONBSSA-N, CAS registry number 33889-69-9 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "diazinon"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey FHIVAFMUCKRCQO-UHFFFAOYSA-N, CAS registry number 333-41-5 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Multimodal Model"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A model capable of processing and generating responses from multiple types of data, such as text, images, and audio."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Incident Postmortem"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A framework for learning from incidents and turning problems into progress by bringing people together to discuss the details of the incident to explore why it happened, its impact, the actions that can be taken to mitigate and resolve it, and the actions to prevent it happen again. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "European Centre for Ecotoxicology and Toxicology of Chemicals"@en-US ; - ncit:C42610 "ECTOC"@en-US ; - dc:description "The European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) is a scientific, non-profit, non-commercial and non-governmental association. Established in 1978, ECETOC's main objective is to identify, evaluate, and through such knowledge help industry to minimise any potentially adverse effects on human health and the environment that may arise from the manufacture and use of chemicals, biomaterials and pharmaceuticals. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Quantitative Structure Activity Relationships"@en-US ; - ncit:C42610 "QSAR"@en-US ; - dc:description "Mathematical models that can be used to predict the physicochemical, biological and environmental fate properties of compounds from the knowledge of their chemical structure."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Identifier"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The unique identifier for an administered item within a registration authority. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "The legislation of 'Registration, Evaluation, Authorisation and Restriction of Chemicals'"@en-US ; - ncit:C42610 "REACH"@en-US ; - dc:description "Regulation (EC) No 1907/2006 of the European Parliament and of the Council concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH). "@en-US . - - - rdf:type owl:Class ; - rdfs:label "3 Rs Principle"@en-US ; - ncit:C42610 "3Rs"@en-US ; - dc:description "Replacement, Reduction, and Refinement. Used in the context of performing more humane animal research."@en-US . - - - rdf:type owl:Class ; - rdfs:label "mancozeb"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "mixture "@en-US . - - - rdf:type owl:Class ; - rdfs:label "pCHEMBL"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A value that allows a number of roughly comparable measures of half-maximal response concentration/potency/affinity to be compared on a negative logarithmic scale. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "SCRUM Master"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A person with the role in the SCRUM method who ensures the team follows the scrum practices and that the backlog, sprint, user stories and epics are clear."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Risk Assessment"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The process of assessing human health risks in a historic, current or emerging exposure scenario for which a concern has risen."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Cloud computing"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A computer infrastructure that provides access to data resources, analysis software, and computer power to conduct analyses specific to a use case or research community. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 2.2"@en-US ; - ncit:C42610 "WP2.2"@en-US ; - dc:description "Disease state - Case study chronic kidney disease: objectives to identify critical physiological pathways, develop AOP networks, test toxicity of selected drugs, and assess the safety of selected drugs."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Resource Description Framework"@en-US ; - ncit:C42610 "RDF"@en-US ; - dc:description "A globally-accepted framework for data and knowledge representation that is intended to be read and interpreted by machines. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "TXG-MAPr R package"@en-US ; - ncit:C42610 "TXG-MAPr"@en-US ; - dc:description "Statistical quantitative AOP approach using known coexpression changes in tissue toxicity."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Monte Carlo Risk Assessment calculation model"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A modeling technique for realistically possible calculation of the intake of risk substances by humans, for example via food, where the exposure can also be linked to the hazard, with which a risk assessment can be carried out."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Regulatory Question"@en-US ; - ncit:C42610 "RQ"@en-US ; - dc:description "A concrete, decision-oriented risk-assessment question, formulated for a given case study, that the Virtual Human Platform should help to answer step-by-step."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Definition of Done"@en-US ; - ncit:C42610 "DoD"@en-US ; - dc:description "A shared understanding among the team of when a task is considered as 'done'. It ensures work is completed to a certain standard before it is accepted. This might include specific documentation, review by another team member or discussion during the Sprint Review."@en-US . - - - og:description "Webpage with the VHP4Safety Glossary"@en-US ; - og:locale "en_US"@en-US ; - og:site_name "glossary"@en-US ; - og:title "VHP4Safety Glossary"@en-US ; - og:type "website"@en-US ; - og:url "https://glossary.vhp4safety.nl/"@en-US ; - dct:title "VHP4Safety Glossary | glossary" ; - - "IE=edge"@en-US ; - - "Webpage with the VHP4Safety Glossary"@en-US ; - - "Jekyll v3.10.0"@en-US ; - - "summary"@en-US ; - - "width=device-width, initial-scale=1"@en-US ; - - ; - "VHP4Safety Glossary"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Template"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A thing that is used as a model for producing other similar examples. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "College ter Beoordeling van Geneesmiddelen"@en-US ; - ncit:C42610 "CBG"@en-US ; - dc:description "Medicines Evaluation Board. The Dutch authority that evaluates and regulates medicines for human and veterinary use. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Physiologically based pharmacokinetic model"@en-US ; - ncit:C42610 "PBPK"@en-US ; - dc:description "Mechanistic representation of ADME processes for a chemical in a living organism, based on physiological and chemical properties"@en-US . - - - rdf:type owl:Class ; - rdfs:label "Strato"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "An internet hosting service provider that supplies the servers where the virtual platform is built. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Integrated Approaches to Testing and Assessment"@en-US ; - ncit:C42610 "IATA"@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "sulfobromophthalein sodium"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey CDTNUNQQEUGDSD-UHFFFAOYSA-L, CAS registry number 123359-42-2 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "α-endosulfan"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey RDYMFSUJUZBWLH-BEJSPLBDSA-N "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Fine-Tuning"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The process of training a pre-existing language model on a smaller, domain-specific dataset to improve its performance on specific tasks or for specific industries."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Knowledge Graphs"@en-US ; - ncit:C42610 "KGs"@en-US ; - dc:description "An organized and graphical representation of real world obejcts and their relationships, represented mostly as nodes and edges, respectively to store data entities and their interrelations. See also Resource Description Framework. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Research Line"@en-US ; - ncit:C42610 "RL"@en-US ; - dc:description "Formal structure within a project to reach some goal."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Research Line 3"@en-US ; - ncit:C42610 "RL3"@en-US ; - dc:description "Implementing the Virtual Human Platform."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Accessible"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "One needs to know how data can be accessed, possibly including authentication and authorisation. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Adverse Outcome"@en-US ; - ncit:C42610 "AO"@en-US ; - dc:description "A specialised type of key event that is generally accepted as being of regulatory significance on the basis of correspondence to an established protection goal or equivalence to an apical endpoint in an accepted regulatory guideline toxicity test. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Developmental and Reproductive Toxicology"@en-US ; - ncit:C42610 "DART"@en-US ; - dc:description ""@en-US . - - - rdf:type owl:Class ; - rdfs:label "Central Access Point"@en-US ; - ncit:C42610 "CAP"@en-US ; - dc:description "A website that provides toxicological risk assessors an easily accessible and structured analysis framework including tools developed within VHP4Safety. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Sprint Planning"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A meeting at the beginning of each sprint where the team selects tasks from the backlog to work on during that sprint. The team will also assign members to each task and discuss how they plan on completing them."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Exposure Assessment"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "The process of assessing the magnitude, frequency and duration of exposure of a certain organism to a certain agent; OF the process of assessing the total external (or internal) exposure following one or more exposure/use scenarios that are described in terms of route, extent, frequency and duration of exposure, including exposure via more than one exposure route (aggregated exposure) and exposure to multiple chemicals (cumulative exposure)."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Technology Readiness Levels"@en-US ; - ncit:C42610 "TRL"@en-US ; - dc:description "TRLs are a method for estimating the maturity of technologies during the acquisition phase of a program. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Work Package 3.1"@en-US ; - ncit:C42610 "WP3.1"@en-US ; - dc:description "Technology Assessment of VHP: objectives to perform technology assessment, study and analyse the initiation, development and implementation of VHP, and specify performance criteria."@en-US . - - - rdf:type owl:Class ; - rdfs:label "Data Management Plan"@en-US ; - ncit:C42610 "DMP"@en-US ; - dc:description "Plans to serve to address the what, how, who, and where of data management by formally outlining the roles, responsibilities, and activities for managing data during and after research in alignment with FAIR principles. "@en-US . - - - rdf:type owl:Class ; - rdfs:label "Dockerfile"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A file that includes the commands to build a Docker image."@en-US . - - - rdf:type owl:Class ; - rdfs:label "No Observed Adverse Effect Level"@en-US ; - ncit:C42610 "NOAEL"@en-US ; - dc:description "The highest exposure level of a chemical stressor evaluated in a toxicity test that shows no harmful effects on a plant or animal."@en-US . - - - rdf:type owl:Class ; - rdfs:label "(External) Exposure (Process Flow Step)"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "A process flow step that is named after exposure assessment and categorizes services that evaluate and analyze the route, duration, magnitude and frequency of exposure of an organism or (sub)population to one or multiple chemicals."@en-US ; - dct:relation . - - - rdf:type owl:Class ; - rdfs:label "iopanoic acid"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "group of stereoisomers, InChIKey OIRFJRBSRORBCM-UHFFFAOYSA-N, CAS registry number 96-83-3 "@en-US . - - - rdf:type owl:Class ; - rdfs:label "(S)-dinoseb"@en-US ; - ncit:C42610 ""@en-US ; - dc:description "type of a chemical entity, InChIKey OWZPCEFYPSAJFR-LURJTMIESA-N "@en-US . - diff --git a/index.md b/index.md index c934b4f..dbe26a1 100644 --- a/index.md +++ b/index.md @@ -23,7 +23,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Process flow steps - +
@@ -65,7 +65,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Chemicals -
Term Abbreviation
+
@@ -76,43 +76,43 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio - + - + - + - + - + - + - + @@ -124,25 +124,25 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio - + - + - + - + @@ -154,31 +154,31 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio - + - + - + - + - + @@ -190,7 +190,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio - + @@ -208,61 +208,61 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio - + - + - + - + - + - + - + - + - +
Term Abbreviation(R)-dinoseb type of a chemical entity, InChIKey OWZPCEFYPSAJFR-ZCFIWIBFSA-N ref1CC[C@@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-] Q415111CC[C@@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-] Q415111CC[C@@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-]
(S)-dinoseb type of a chemical entity, InChIKey OWZPCEFYPSAJFR-LURJTMIESA-N ref1CC[C@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-] Q415111CC[C@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-] Q415111CC[C@H](C)C1=CC(=CC(=C1O)[N+](=O)[O-])[N+](=O)[O-]
amiodarone chemical compound, InChIKey IYIKLHRQXLHMJQ-UHFFFAOYSA-N, CAS registry number 1951-25-3 ref1CCCCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)I)OCCN(CC)CC)ICCCCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)I)OCCN(CC)CC)ICCCCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)I)OCCN(CC)CC)I
amiodarone hydrochloride type of a chemical entity, InChIKey ITPDYQOUSLNIHG-UHFFFAOYSA-N, CAS registry number 19774-82-4 ref1Cl[H].CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1Cl[H].CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1Cl[H].CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1
cefuroxime type of a chemical entity, InChIKey JFPVXVDWJQMJEE-IZRZKJBUSA-N, CAS registry number 55268-75-2 ref1[H][C@]12SCC(COC(N)=O)=C(N1C(=O)[C@H]2NC(=O)\C(=N/OC)c3ccco3)C(O)=O[H][C@]12SCC(COC(N)=O)=C(N1C(=O)[C@H]2NC(=O)\C(=N/OC)c3ccco3)C(O)=O[H][C@]12SCC(COC(N)=O)=C(N1C(=O)[C@H]2NC(=O)\C(=N/OC)c3ccco3)C(O)=O
chlorpyrifos type of a chemical entity, InChIKey SBPBAQFWLVIOKP-UHFFFAOYSA-N, CAS registry number 2921-88-2 ref1CCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)ClCCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)ClCCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)Cl
diazinon type of a chemical entity, InChIKey FHIVAFMUCKRCQO-UHFFFAOYSA-N, CAS registry number 333-41-5 ref1CCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)CCCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)CCCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)C
dinoseb endosulfan mixture, InChIKey RDYMFSUJUZBWLH-AZVNHNRSSA-N ref1Cl[C@]12C(=C([C@]([C@@H]3COS(OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@]12C(=C([C@]([C@@H]3COS(OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@]12C(=C([C@]([C@@H]3COS(OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)Cl
ethylenebis(dithiocarbamate) type of a chemical entity, InChIKey AWYFNIZYMPNGAI-UHFFFAOYSA-L ref1C(CNC(=S)[S-])NC(=S)[S-]C(CNC(=S)[S-])NC(=S)[S-]C(CNC(=S)[S-])NC(=S)[S-]
iopanoic acid group of stereoisomers, InChIKey OIRFJRBSRORBCM-UHFFFAOYSA-N, CAS registry number 96-83-3 ref1CCC(CC1=C(C(=C(C=C1I)I)N)I)C(=O)OCCC(CC1=C(C(=C(C=C1I)I)N)I)C(=O)OCCC(CC1=C(C(=C(C=C1I)I)N)I)C(=O)O
lesinurad chemical compound, InChIKey FGQFOYHRJSUHMR-UHFFFAOYSA-N, CAS registry number 878672-00-5 ref1C1CC1C2=CC=C(C3=CC=CC=C23)N4C(=NN=C4Br)SCC(=O)OC1CC1C2=CC=C(C3=CC=CC=C23)N4C(=NN=C4Br)SCC(=O)OC1CC1C2=CC=C(C3=CC=CC=C23)N4C(=NN=C4Br)SCC(=O)O
mancozeb Mn²⁺ type of a chemical entity, InChIKey WAEMQWOKJMHJLA-UHFFFAOYSA-N ref1[Mn+2][Mn+2][Mn+2]
monobutyl phthalate MBP type of a chemical entity, InChIKey YZBOVSFWWNVKRJ-UHFFFAOYSA-N, CAS registry number 131-70-4 ref1CCCCOC(=O)c1ccccc1C(O)=OCCCCOC(=O)c1ccccc1C(O)=OCCCCOC(=O)c1ccccc1C(O)=O
NH-3 chemical compound, InChIKey IXMROOKFPWGDGF-UHFFFAOYSA-N, CAS registry number 447415-26-1 ref1CC1=CC(=CC(=C1CC2=CC(=C(C(=C2)C#CC3=CC=C(C=C3)[N+](=O)[O-])O)C(C)C)C)OCC(=O)OCC1=CC(=CC(=C1CC2=CC(=C(C(=C2)C#CC3=CC=C(C=C3)[N+](=O)[O-])O)C(C)C)C)OCC(=O)OCC1=CC(=CC(=C1CC2=CC(=C(C(=C2)C#CC3=CC=C(C=C3)[N+](=O)[O-])O)C(C)C)C)OCC(=O)O
PBDE-99 type of a chemical entity, InChIKey WHPVYXDFIXRKLN-UHFFFAOYSA-N, CAS registry number 60348-60-9 ref1C1=CC(=C(C=C1Br)Br)OC2=CC(=C(C=C2Br)Br)BrC1=CC(=C(C=C1Br)Br)OC2=CC(=C(C=C2Br)Br)BrC1=CC(=C(C=C1Br)Br)OC2=CC(=C(C=C2Br)Br)Br
rotenone chemical compound, InChIKey JUVIOZPCNVVQFO-HBGVWJBISA-N, CAS registry number 83-79-4 ref1CC(=C)[C@H]1CC2=C(O1)C=CC3=C2O[C@@H]4COC5=CC(=C(C=C5[C@@H]4C3=O)OC)OCCC(=C)[C@H]1CC2=C(O1)C=CC3=C2O[C@@H]4COC5=CC(=C(C=C5[C@@H]4C3=O)OC)OCCC(=C)[C@H]1CC2=C(O1)C=CC3=C2O[C@@H]4COC5=CC(=C(C=C5[C@@H]4C3=O)OC)OC
Silibinin silychristin A chemical compound, InChIKey BMLIIPOXVWESJG-LMBCONBSSA-N, CAS registry number 33889-69-9 ref1COC1=C(C=CC(=C1)[C@H]2[C@@H](C3=C(O2)C(=CC(=C3)[C@@H]4[C@H](C(=O)C5=C(C=C(C=C5O4)O)O)O)O)CO)OCOC1=C(C=CC(=C1)[C@H]2[C@@H](C3=C(O2)C(=CC(=C3)[C@@H]4[C@H](C(=O)C5=C(C=C(C=C5O4)O)O)O)O)CO)OCOC1=C(C=CC(=C1)[C@H]2[C@@H](C3=C(O2)C(=CC(=C3)[C@@H]4[C@H](C(=O)C5=C(C=C(C=C5O4)O)O)O)O)CO)O
silymarin sulfobromophthalein type of a chemical entity, InChIKey OHTXTCNTQJFRIG-UHFFFAOYSA-N, CAS registry number 297-83-6 ref1Oc1ccc(cc1S(O)(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S(O)(=O)=OOc1ccc(cc1S(O)(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S(O)(=O)=OOc1ccc(cc1S(O)(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S(O)(=O)=O
sulfobromophthalein sodium type of a chemical entity, InChIKey CDTNUNQQEUGDSD-UHFFFAOYSA-L, CAS registry number 123359-42-2 ref1[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O
T3 T3 type of a chemical entity, InChIKey AUYYCJSJGJYCDS-LBPRGKRZSA-N ref1N[C@@H](Cc1cc(I)c(Oc2ccc(O)c(I)c2)c(I)c1)C(O)=ON[C@@H](Cc1cc(I)c(Oc2ccc(O)c(I)c2)c(I)c1)C(O)=ON[C@@H](Cc1cc(I)c(Oc2ccc(O)c(I)c2)c(I)c1)C(O)=O
T4 T4 type of a chemical entity, InChIKey XUIIKFGFIJCVMT-LBPRGKRZSA-N ref1N[C@@H](Cc1cc(I)c(Oc2cc(I)c(O)c(I)c2)c(I)c1)C(O)=ON[C@@H](Cc1cc(I)c(Oc2cc(I)c(O)c(I)c2)c(I)c1)C(O)=ON[C@@H](Cc1cc(I)c(Oc2cc(I)c(O)c(I)c2)c(I)c1)C(O)=O
tetrabromobisphenol A TBBPA bisphenol, InChIKey VEORPZCZECFIRK-UHFFFAOYSA-N, CAS registry number 79-94-7 ref1CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C2=CC(=C(C(=C2)Br)O)BrCC(C)(C1=CC(=C(C(=C1)Br)O)Br)C2=CC(=C(C(=C2)Br)O)BrCC(C)(C1=CC(=C(C(=C1)Br)O)Br)C2=CC(=C(C(=C2)Br)O)Br
xanthohumol type of a chemical entity, InChIKey ORXQGKIUCDPEAJ-YRNVUSSQSA-N, CAS registry number 6754-58-1 ref1COc1cc(O)c(C\C=C(/C)C)c(O)c1C(=O)\C=C\c2ccc(O)cc2COc1cc(O)c(C\C=C(/C)C)c(O)c1C(=O)\C=C\c2ccc(O)cc2COc1cc(O)c(C\C=C(/C)C)c(O)c1C(=O)\C=C\c2ccc(O)cc2
Zn²⁺ type of a chemical entity, InChIKey PTFCDOFLOPIGGS-UHFFFAOYSA-N ref1[Zn+2][Zn+2][Zn+2]
α-endosulfan type of a chemical entity, InChIKey RDYMFSUJUZBWLH-BEJSPLBDSA-N ref1Cl[C@@]12C(=C([C@@]([C@@H]3CO[S@@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@@]12C(=C([C@@]([C@@H]3CO[S@@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@@]12C(=C([C@@]([C@@H]3CO[S@@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)Cl
β-endosulfan type of a chemical entity, InChIKey RDYMFSUJUZBWLH-LLXUDWAZSA-N ref1Cl[C@]12C(=C([C@]([C@@H]3CO[S@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@]12C(=C([C@]([C@@H]3CO[S@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)ClCl[C@]12C(=C([C@]([C@@H]3CO[S@](OC[C@@H]31)=O)(C2(Cl)Cl)Cl)Cl)Cl
## Toxicology in General - +
@@ -374,7 +374,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Risk assessment-related terms -
Term Abbreviation
+
@@ -455,7 +455,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Adverse Outcome Pathway-related terms -
Term Abbreviation
+
@@ -517,7 +517,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Server-related terms -
Term Abbreviation
+
@@ -593,7 +593,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Tool/service-related terms -
Term Abbreviation
+
@@ -959,7 +959,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Project-related terms -
Term Abbreviation
+
@@ -1075,7 +1075,7 @@ Experienced GitHub users are encouraged to submit pull requests. More informatio ## Organizations -
Term Abbreviation
+
diff --git a/scripts/template_to_md.py b/scripts/template_to_md.py index 51d77bc..c554d73 100644 --- a/scripts/template_to_md.py +++ b/scripts/template_to_md.py @@ -14,6 +14,7 @@ "ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#", "dc": "http://purl.org/dc/elements/1.1/", "dcterms": "http://purl.org/dc/terms/", + "chebi": "http://purl.obolibrary.org/obo/chebi/", "vhp": "https://vhp4safety.github.io/glossary#", } @@ -67,7 +68,11 @@ def encode_smiles(smiles): image_html = f'{smiles}' return image_html + # Preserve original SMILES values (just the SMILES part, without Wikidata ID) if "SMILES" in df.columns: + df["SMILES_original"] = df["SMILES"].apply( + lambda x: x.split(" ")[0].strip() if isinstance(x, str) and " " in x else (x.strip() if isinstance(x, str) else "") + ) df["SMILES"] = df.apply( lambda row: encode_smiles(row["SMILES"]) if isinstance(row["SMILES"], str) else "", axis=1 ) @@ -79,8 +84,8 @@ def encode_smiles(smiles): f'
Term Abbreviation
\n' ) - # Adjusted headers to use \n" + "".join([f" \n" for header in headers]) @@ -122,6 +127,18 @@ def encode_smiles(smiles): table_html += f' \n' else: table_html += " \n" + elif header.lower() == "smiles": + # Add SMILES with RDFa property using original SMILES value + # Use full URI in property attribute with text content + if cell_value: + original_smiles = str(row.get("SMILES_original", "")).strip() + if original_smiles: + smiles_prop = "http://purl.obolibrary.org/obo/chebi/smiles" + table_html += f' \n' + else: + table_html += f" \n" + else: + table_html += " \n" else: table_html += f" \n"
with - headers = [header for header in df.columns if header != "ID"] + # Adjusted headers to use with , excluding ID and SMILES_original + headers = [header for header in df.columns if header not in ["ID", "SMILES_original"]] table_html += ( "
{header}{SVG_ICON} {vhp_id}{cell_value}{original_smiles}{cell_value}{cell_value}