Adding tools and links to the text

data-description/human-clinical-and-health-data.md

@@ -80,7 +80,7 @@ Metadata is essential in infectious disease settings for:
     * {% tool "schema-org" %} is a metadata standard that helps search engines index web pages. It improves the machine-readability of the pages and so increases the discoverability of datasets. Schema.org tags also add semantics, and allow search engines to understand the type of content available on the web page.
  * Standards such as HL7 and OMOP provide consistent frameworks for data representation. These standards ensure that health data is formatted and structured in a way that allows for seamless sharing and integration across different healthcare systems and studies.
     * HL7 (Health Level Seven International): HL7 is a set of international standards for the exchange, integration, sharing, and retrieval of electronic health information. It provides a framework for managing clinical and administrative data. While HL7 includes some ontological components, it is primarily a set of standards rather than a pure ontology.
-    * OMOP (Observational Medical Outcomes Partnership): OMOP is a standardised data model and common data vocabulary. It is designed to facilitate the analysis of disparate observational healthcare databases, to improve the assessment of healthcare outcomes and safety. It goes beyond an ontological component (the OMOP Common Data Model and Vocabulary), and encompasses data standardisation and analytics frameworks.
+    * [OMOP (Observational Medical Outcomes Partnership)](https://ohdsi.github.io/CommonDataModel/): OMOP is a standardised data model and common data vocabulary. It is designed to facilitate the analysis of disparate observational healthcare databases, to improve the assessment of healthcare outcomes and safety. It goes beyond an ontological component (the OMOP Common Data Model and Vocabulary), and encompasses data standardisation and analytics frameworks.
 
 ### Ontologies
 An ontology is a formal description of knowledge as a set of concepts within a domain, and the relationships that exist between them. It ensures a common understanding of information and makes explicit domain assumptions, thus allowing organisations to make better sense of their data ([Fundamentals, O. (2022, December 16)](https://www.ontotext.com/knowledgehub/fundamentals/what-are-ontologies/#:~:text=An%20ontology%20is%20a%20formal,better%20sense%20of%20their%20data)). 
@@ -101,9 +101,9 @@ When developing and using health data ontologies, consider the following:
 
  * For interoperability, standardisation is essential for maintaining consistency and accuracy in data representation, which can be achieved by utilising widely accepted vocabularies like ICD-10 and SNOMED CT.
  * Tools like the Ontology Lookup Service (OLS) and NCBO BioPortal provide access to various biomedical ontologies, supporting standardisation efforts and improving data quality and utility. These resources help researchers and healthcare providers ensure that their data adheres to the highest standards of accuracy and consistency.
-    * [NCBO BioPortal](http://bioportal.bioontology.org/): NCBO BioPortal is an extensive repository and web-based platform that provides access to a wide array of biomedical ontologies and terminologies, enabling users to search, browse, and utilise these resources for research and data annotation purposes.
-    * [Ontology Lookup Service (OLS)](http://www.ebi.ac.uk/ontology-lookup/): The Ontology Lookup Service (OLS) is a web-based tool that provides a single point of access to multiple ontologies, enabling users to search and browse a wide range of biomedical and health-related terminologies and ontologies.
-    * [OBO Foundry](http://www.obofoundry.org/): The OBO Foundry is a collaborative initiative that aims to develop a family of interoperable ontologies designed for biomedical science. It provides principles and best practices for ontology development. These ensure that ontologies are logically well-formed, scientifically accurate, and useful for data integration across different biological and medical domains.
+    * {% tool "bioportal" %}: NCBO BioPortal is an extensive repository and web-based platform that provides access to a wide array of biomedical ontologies and terminologies, enabling users to search, browse, and utilise these resources for research and data annotation purposes.
+    * {% tool "ols" %}: The Ontology Lookup Service (OLS) is a web-based tool that provides a single point of access to multiple ontologies, enabling users to search and browse a wide range of biomedical and health-related terminologies and ontologies.
+    * {% tool "the-open-biological-and-biomedical-ontology-foundry" %}: The OBO Foundry is a collaborative initiative that aims to develop a family of interoperable ontologies designed for biomedical science. It provides principles and best practices for ontology development. These ensure that ontologies are logically well-formed, scientifically accurate, and useful for data integration across different biological and medical domains.
     * ICD-10 is a medical classification system maintained by the World Health Organization (WHO). It provides codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. It serves as a comprehensive ontology for clinical diagnoses and health conditions, enabling standardised recording and reporting of health information across different healthcare systems.
 
 By adhering to these standards and ontologies, healthcare providers and researchers can improve data management, leading to better disease tracking, treatment outcomes, and public health responses.
@@ -133,10 +133,10 @@ Handling health data, especially in the context of infectious diseases, requires
  * The use of [blockchain technology in Estonia’s digital healthcare](https://e-estonia.com/blockchain-healthcare-estonian-experience/) system enhances the security of health data by creating tamper-proof records for every patient encounter.
  * [The WHO’s Global Influenza Surveillance and Response System (GISRS)](https://www.who.int/initiatives/global-influenza-surveillance-and-response-system) provides standardised testing procedures and reagents to laboratories worldwide, ensuring the accuracy and reliability of influenza data globally.
  * Data should be shared as openly and as rapidly as possible, for example by uploading SARS-CoV-2 sequence to [The European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena/browser/home). ENA  is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. 
- * [The GISAID](https://gisaid.org/) Data Science Initiative platform promotes the rapid sharing of data, from priority pathogens including influenza, hCoV-19, respiratory syncytial virus (RSV), hMpxV as well as arboviruses including chikungunya, dengue and zika. It includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses. However, GISAID is much more restrictive on data reuse compared to ENA, for example. 
+ * {% tool "gsaid"%} Data Science Initiative platform promotes the rapid sharing of data, from priority pathogens including influenza, hCoV-19, respiratory syncytial virus (RSV), hMpxV as well as arboviruses including chikungunya, dengue and zika. It includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses. However, GISAID is much more restrictive on data reuse compared to ENA, for example. 
  * The European Union’s General Data Protection Regulation (GDPR) includes specific provisions for processing health data, such as requiring explicit consent from individuals and allowing data processing when necessary for reasons of public interest. Please also take into account local laws and regulations.
  * During the Ebola outbreak in West Africa, [ethical guidelines](https://bioethics.jhu.edu/wp-content/uploads/2019/03/Ethics20Guidance20for20Public20Health20Containment20Lessons20from20Ebola_April2019.pdf ) for data sharing were established that balanced the need for rapid data sharing with the need to protect communities and individuals from harm, addressing issues like consent and the potential for stigmatization.
  * [European Centre for Disease Prevention and Control (CDC)](https://www.ecdc.europa.eu/en) regularly publishes detailed reports and datasets on its website regarding disease outbreaks and surveillance data, improving transparency and helping to maintain public trust.
- * Health Level Seven International (HL7) and Fast Healthcare Interoperability Resources (FHIR) are standards that facilitate the exchange of healthcare information electronically, allowing different health information systems to work together more effectively.
+ * [Health Level Seven International (HL7)](https://www.hl7.org/) and Fast Healthcare Interoperability Resources (FHIR) are standards that facilitate the exchange of healthcare information electronically, allowing different health information systems to work together more effectively.
  * The use of Electronic Health Records (EHRs) integrated with real-time alerting systems has been implemented in hospitals to flag potential infectious disease cases based on symptoms and travel history, enabling prompt isolation and treatment.