From a285a582a14da46a37c651817cabc8227bea5624 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mat=C3=BA=C5=A1=20Kala=C5=A1?= <matus.kalas@uib.no>
Date: Thu, 2 Sep 2021 20:59:15 +0200
Subject: [PATCH] Dusted off & fixed links and some text
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* Fixed old links that never worked, fixes #12. Thanks @Pfeil for spotting! 🙏🏽
* Updated some related texts.
* Changed most links to **https**. Is this what we want, or not? (Similarly to the suggested https://github.com/edamontology/edamontology/pull/699)
* Slighly updated the main (top) description.

Co-authored-by: Pfeil <Pfeil@users.noreply.github.com>
---
 page.html | 69 +++++++++++++++++++++++++++----------------------------
 1 file changed, 34 insertions(+), 35 deletions(-)

diff --git a/page.html b/page.html
index 10ac175..c8b468f 100644
--- a/page.html
+++ b/page.html
@@ -119,13 +119,13 @@
 
 
 <!--header-panel
-# EDAM - Ontology of bioscientific data analysis
+# EDAM - Ontology of bioscientific data analysis and data management
 -->
 
 <!--content-panel
-EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and [bioimage informatics](https://github.com/edamontology/edam-bioimaging). EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use (see figures below).
+EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management (including computational biology, bioinformatics, and [bioimage informatics](https://github.com/edamontology/edam-bioimaging)). EDAM includes topics, operations, types of data and data identifiers, and data formats, relevant in data analysis and data management in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use (see figures below).
 
-EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to bioscientific data analysis: _e.g._ tools, workflows, or training materials. EDAM is also useful in data management, for recording provenance metadata of processed bioscientific data.
+EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to data analysis and management: _e.g._ tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed bioscientific data.
 
 EDAM is a community project and its development can be followed and contributed to at [GitHub](https://github.com/edamontology/edamontology).
 
@@ -134,9 +134,9 @@
 
 EDAM can be graphically browsed online at:
 
-*   [NCBO ontology browser (BioPortal)](http://bioportal.bioontology.org/ontologies/EDAM?p=classes) (all-newest unstable version)
-*   [EBI Ontology Look-up Service (OLS)](http://www.ebi.ac.uk/ols/ontologies/edam) (latest stable version)
-*   [EDAM Browser](https://edamontology.github.io/edam-browser/) (<b>new:</b> all versions<b>!</b>)
+*   [NCBO ontology browser (BioPortal)](https://bioportal.bioontology.org/ontologies/EDAM?p=classes) (all-newest _unstable_ version)
+*   [EBI Ontology Look-up Service (OLS)](https://www.ebi.ac.uk/ols/ontologies/edam) (latest **stable** version)
+*   [EDAM Browser](https://edamontology.github.io/edam-browser/) (<b>new: all versions!</b>)
 *   WebProtégé (free registration required)
     *   [Unstable development version](https://webprotege.stanford.edu/#projects/4befad5f-f27b-430c-a07d-fcf635093169/edit/Classes)
     *   [Always the latest stable version](https://webprotege.stanford.edu/#projects/98640503-a37d-4404-84da-caf30fadd685/edit/Classes)
@@ -150,37 +150,37 @@
 
 
 ##   <p></p><a id="Download"></a>Downloads
-[http://edamontology.org/EDAM_dev.owl](http://edamontology.org/EDAM_dev.owl) (The all-newest unstable version)
+[https://edamontology.org/EDAM_dev.owl](https://edamontology.org/EDAM_dev.owl) (The all-newest, _unstable_ released version)
 
-[<b>http://edamontology.org/EDAM_1.25.owl</b>](http://edamontology.org/EDAM_1.25.owl) (The latest stable version is at the moment <b>1.25</b>)
+[<b>https://edamontology.org/EDAM_1.25.owl</b>](https://edamontology.org/EDAM_1.25.owl) (The latest **stable** version is at the moment <b>1.25</b>)
 
-[<b>http://edamontology.org/EDAM.owl</b>](http://edamontology.org/EDAM.owl) (Always the latest stable version, in OWL format)
+[<b>https://edamontology.org/EDAM.owl</b>](https://edamontology.org/EDAM.owl) (Always the latest stable version, in OWL format)
 
-[<b>http://edamontology.org/EDAM_1.25.tsv</b>](http://edamontology.org/EDAM_1.25.tsv) (Stable version <b>1.25</b>, as tab-separated values (TSV))
+[<b>https://edamontology.org/EDAM_1.25.tsv</b>](https://edamontology.org/EDAM_1.25.tsv) (Stable version <b>1.25</b>, as tab-separated values (TSV))
 
-[<b>http://edamontology.org/EDAM.tsv</b>](http://edamontology.org/EDAM.tsv) (Always the latest stable version, in TSV format)
+[<b>https://edamontology.org/EDAM.tsv</b>](https://edamontology.org/EDAM.tsv) (Always the latest stable version, in TSV format)
 
-[<b>http://edamontology.org/EDAM_1.25.csv</b>](http://edamontology.org/EDAM_1.25.csv) (Stable version <b>1.25</b>, as comma-separated values (CSV))
+[<b>https://edamontology.org/EDAM_1.25.csv</b>](https://edamontology.org/EDAM_1.25.csv) (Stable version <b>1.25</b>, as comma-separated values (CSV))
 
-[<b>http://edamontology.org/EDAM.csv</b>](http://edamontology.org/EDAM.csv) (Always the latest stable version, in CSV format)
+[<b>https://edamontology.org/EDAM.csv</b>](https://edamontology.org/EDAM.csv) (Always the latest stable version, in CSV format)
 
-[http://edamontology.org/EDAM.obo](http://edamontology.org/EDAM.obo) (The last version available in OBO format is an ancient EDAM version <b>1.2</b>. Because the conversion from OWL to OBO hasn't yet fully been automated for EDAM, we will only resume providing OBO format in case of substantial demand. In that case, please contact us via [issues](https://github.com/edamontology/edamontology/issues/new).)
+[https://edamontology.org/EDAM.obo](https://edamontology.org/EDAM.obo) (The last version available in OBO format is an ancient EDAM version <b>1.2</b>. Because the conversion from OWL to OBO hasn't yet fully been automated for EDAM, we will only resume providing OBO format in case of substantial demand. In that case, please contact us via [issues](https://github.com/edamontology/edamontology/issues/new).)
 
 [https://github.com/edamontology/edamontology/releases](https://github.com/edamontology/edamontology/releases) (All stable releases of EDAM)
 
-[https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl](https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl) (Unstable development version)
+[https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl](https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl) (Unreleased development version)
 
 
 ##   <p></p><a id="Documentation"></a>Documentation
 
-Comprehensive documentation and guidelines are available on [ReadTheDocs](http://edamontologydocs.readthedocs.io/en/latest/index.html) (maintained [here](http://edamontologydocs.readthedocs.io/en/latest/)).
+Comprehensive documentation and guidelines are available on [ReadTheDocs](https://edamontologydocs.readthedocs.io/en/latest/index.html) (maintained [here](https://github.com/edamontology/edamontologyDocs)).
 
 
 
 ##   <p></p><a id="Contacts"></a>Contacts
 
 
-<b>Twitter:</b> [@edamontology](http://twitter.com/edamontology) ([follow](https://twitter.com/intent/follow?original_referer=http%3A%2F%2Fedamontology.org&region=follow_link&screen_name=edamontology&tw_p=followbutton)).
+<b>Twitter:</b> [@edamontology](https://twitter.com/edamontology) ([follow](https://twitter.com/intent/follow?original_referer=http%3A%2F%2Fedamontology.org&region=follow_link&screen_name=edamontology&tw_p=followbutton)).
 
 All development, and the preferred request and discussion channel is <b>GitHub:</b> [https://github.com/edamontology/edamontology](https://github.com/edamontology/edamontology)
 
@@ -190,41 +190,40 @@
 
 ##   <p></p><a id="Scope"></a>Scope
 
-EDAM includes 4 main sub-ontologies or 'branches' of concepts:
+EDAM includes 4 main sections of concepts (sub-ontologies):
 
-*   _**Data**_ - “Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.”
-*   _**Format**_ - “A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.”
-*   _**Operation**_ - “A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).”
-*   _**Topic**_ - “A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.”
+*   _**[Topic](https://edamontology.org/topic_0003)**_ - “A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.”
+*   _**[Operation](https://edamontology.org/operation_0004)**_ - “A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).”
+*   _**[Data](https://edamontology.org/data_0006)**_ - “Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.”
+*   _**[Format](https://edamontology.org/format_1915)**_ - “A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.”
 
-Noteworthy sub-branch:
-*   _**Data->Identifier**_ - “A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).”
+Noteworthy sub-section:
+*   _**Data -> [Identifier](https://edamontology.org/data_0842)**_ - “A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).”
 
 <img alt="EDAM concepts" src="EDAMconcepts.png" style="max-height: 36em; max-width: 94%">
 
-_**EDAM concepts.** Boxes indicate sub-ontologies in EDAM, with example concepts._
-
-As a general rule, the _**Data**_, _**Format**_, and _**Operation**_ branches include concepts strictly in domain of bioinformatics and computational biology: concepts purely concerning biology, computer science _etc._ are not included. The _**Topic**_ branch includes broader inter-disciplinary concepts from the biological and medical domains.
+_**EDAM concepts.** Boxes indicate sections (sub-ontologies) of EDAM, with example concepts._
 
 
 
 ##   <p></p><a id="Architecture"></a>Architecture
 
-EDAM has 3 types of content:
+EDAM includes 4 types of content:
 
-*   [Concepts](concepts.html) - All concepts have a name (the term or label) and definition. Further, a concept may have simple relations to other EDAM concepts, as well other intrinsic properties, _e.g._ an identifier may have a regular expression defining its syntax.
-*   [Hierarchy](relations.html#is_a) - Every concept (excluding top-level concepts) is related to one or more other concepts within the same branch by an _**is a**_ relation (specialisation). Hence EDAM has 4 primary hierarchies (for _Data_, _Format_, _Operation_, and _Topic_).
-*   [Relations](relations.html) - Concepts are related by defined relation types (see illustration below), which reflect well established or self-evident principles, and are used to define internal consistency of EDAM.
+*   __Concepts__ - All concepts have a name (the term or label) and definition. Further, a concept may have simple relations to other EDAM concepts, as well other intrinsic properties, _e.g._ an identifier may have a regular expression defining its syntax.
+*   __[Hierarchy](https://bioportal.bioontology.org/ontologies/EDAM?p=classes)__ - Every concept (excluding the top level) is related to one or more other concepts within the same section of EDAM by a specialisation/generalisation relation (subsumption, _**is a**_), forming a _directed acyclic graph_ (DAG). Hence EDAM consists of 4 primary hierarchies (connected DAGs), for the 4 main sections: _**Topic**_, _**Operation**_, _**Data**_, and _**Format**_.
+*   __[Relations](relations-and-properties.html)__ - In addition to the hierarchy, concepts in EDAM can be related with each other by additional types of relations (see illustration below). These supplement the definitions of concepts and strengthen internal consistency of EDAM. They can be used also outside of EDAM, for example in annotated data.
+*   __[Properties](relations-and-properties.html)__ - In addition to standardised attributes such a primary term and a definition, some concepts in EDAM contain additional information, _e.g._ a link to the documentation of a _**Format**_, or a regular expression for an _**Identifier**_. EDAM includes the definitions of these properties (attributes) which can also be used outside of EDAM. 
 
 <img alt="EDAM relations" src="EDAMrelations.png" style="max-height: 36em; max-width: 94%">
 
-_**EDAM architecture is simple.** Boxes indicate top-level concepts (sub-ontologies), and lines indicate types of relations._
+_**EDAM architecture is simple.** Boxes indicate top-level concepts (sections, sub-ontologies), and lines indicate types of relations._
 
 
 ##   <p></p><a id="License"></a>Licence
 
-[![Creative Commons Licence](https://i.creativecommons.org/l/by-sa/4.0/88x31.png)](http://creativecommons.org/licenses/by-sa/4.0/)
-[EDAM](http://edamontology.org) is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/) (CC BY-SA 4.0).
+[![Creative Commons Licence](https://i.creativecommons.org/l/by-sa/4.0/88x31.png)](https://creativecommons.org/licenses/by-sa/4.0/)
+[EDAM](https://github.com/edamontology/edamontology) is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-sa/4.0/) (CC BY-SA 4.0).
 
 We recommend, however, that while EDAM is being actively maintained by its authors, substantial derived work, major modifications (especially conceptual and semantic), and re-definitions of concepts and other content (_e.g._ additional constraints on EDAM concepts/`owl:Class`-es within `owl:imports` meant with universal validity, that would "close" some desired options of the open-world assumption) are consulted with the EDAM core developers beforehand at the time of consideration, and consistent solutions are sought in collaboration.
 
@@ -233,7 +232,7 @@
 EDAM is described in the following article. If you use, or refer to EDAM or its part, please cite:
 
 *   Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (2013). [EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats](http://bioinformatics.oxfordjournals.org/content/29/10/1325.full). _Bioinformatics_, **29**(10): 1325-1332.
-DOI: [10.1093/bioinformatics/btt113](http://doi.org/10.1093/bioinformatics/btt113)   PMID: [23479348](http://www.ncbi.nlm.nih.gov/pubmed/23479348)    The article is freely available without restrictions (Open access)
+DOI: [10.1093/bioinformatics/btt113](https://doi.org/10.1093/bioinformatics/btt113)   PMID: [23479348](https://www.ncbi.nlm.nih.gov/pubmed/23479348)    The article is freely available without restrictions (Open access)