obophenotype · matentzn · Jul 26, 2024 · Aug 1, 2024 · Aug 1, 2024
diff --git a/docs/community/workshops.md b/docs/community/workshops.md
@@ -1,25 +1,26 @@
-# Workshops
-
-Since its inception in 2008, the HPO has conducted numerous workshops  (“hackathons”) with clinical experts to add content to the HPO for specific areas of medicine. Please contact the HPO team if you would like to work with us on HPO terms for an area of medicine.
-
-Participants in such workshops are invited to join the HPO team as coauthors in our regular database update articles (e.g., [PMID:24217912](https://pubmed.ncbi.nlm.nih.gov/24217912/), [PMID:27899602](https://pubmed.ncbi.nlm.nih.gov/27899602/), [PMID:33264411](https://pubmed.ncbi.nlm.nih.gov/33264411/), [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/)). Additionally, some collaborative groups have published focussed aarticles about the work to which the HPO team has contributed. These many contributions (and many others not listed here) have enormously contributed to the quality of the HPO.
-
-
-| Date        | Location                            | Topic |Coordination |
-| :---------- | :----------------------------------- | :---------- | :---------- |
-| 2009 | Sanger Institute, Hinxton, England | General review (5 day workshop with multiple topics)| [Helen Firth](https://www.sanger.ac.uk/external_person/firth-helen/){target="_blank"}, [DECIPHER consortium](https://www.deciphergenomics.org/){target="_blank"} |
-| 2012 |Charité - Universitätsmedizin Berlin, Germany |2-day workshop in Berlin, Germany, to extend dental terminology in the HPO |Prof. [Isabelle Bailleul-Forestier](https://www.eugenol.com/profils/pr-isabelle-bailleul-forestier-698){target="_blank"} (Paul Sabatier University - Toulouse, France) |
-| 2012-2016 | Work to add 80 terms and associated is-a relationships were added to HPO (See [PMID:25949529](https://www.ncbi.nlm.nih.gov/pubmed/25949529){target="_blank"}) | Abnormal bleeding  |[BRIDGE BPD Consortium](https://www.science.org/content/author/bridge-bpd-consortium){target="_blank"}, Prof. Willem Ouwehand, University of Cambridge  | 
-|2013| Charité - Universitätsmedizin Berlin, Germany |  Epilepsy phenotypes and EEG abnormalities | [Prof. Ingo Helbig](https://www.epilepsiegenetik.de/%C3%BCber-uns/ingo-helbig/){target="_blank"}  | 
-|2015|Cambridge, England |Workshop with the UK's National Institute for Health Research (NIHR) Rare Disease—Translational Research Collaboration (See [PMID:27899602](https://pubmed.ncbi.nlm.nih.gov/27899602/){target="_blank"})|Patrick Chinnery, Mareike Veltman and Roger James.|
-|2017| [National Institute for Allergy and Infectious Diseases (NIAID-NIH)](https://www.niaid.nih.gov/){target="_blank"}|Immunology| [Morgan Similuk](https://www.linkedin.com/in/morgan-butrick-similuk-66397314/){target="_blank"} |
-|2017|[Stanford University](https://www.stanford.edu/){target="_blank"} | Cardiology | [Matthew Wheeler](https://med.stanford.edu/profiles/9086){target="_blank"} |
-|2017| Mont St. Odile, France | Ophthalmology (See [PMID:30626441](https://pubmed.ncbi.nlm.nih.gov/30626441/){target="_blank"} | Panagiotis Sergouniotis, [European Reference Network for Rare Eye Diseases](https://www.ern-eye.eu/){target="_blank"} |
-|2017-2024| Ongoing onsite and virtual workshops | Nephrology (see [PMID:32939051](https://pubmed.ncbi.nlm.nih.gov/32939051/){target="_blank"} ) | [Kidney Precision Medicine Project](https://www.kpmp.org/){target="_blank"}  (KPMP) |
-|2019-2021|Three workshops, numerous teleconferences, and joint task forces|Inborn errors of immunity (IEI)|[ESID (European Society for Immunodeficiencies)](https://esid.org/)|
-|2017-2023|numerous teleconferences| Pulmonology (See [PMID:36588100](https://pubmed.ncbi.nlm.nih.gov/36588100/){target="_blank"})| [ChILD EU](https://www.ersnet.org/science-and-research/clinical-research-collaboration-application-programme/child-eu/), Matthias Griese |
-|2017| numerous teleconferences | Newborn screening (See [PMID:33264411](https://pubmed.ncbi.nlm.nih.gov/33264411/){target="_blank"})|  Newborn Screening Translational Research Network (NBSTRN), Amy Brower |
-
-
-
-
+# Workshop List
+
+| Date | Location | Topic | Coordination | Status |
+| ---- | -------- | ----- | ------------ | ------ |
+| 9/1/2012 | Berlin, Germany | HPO-Dental |  Prof. Isabelle Bailleul-Forestier (Paul Sabatier University - Toulouse, France) | Complete |
+| 8/1/2009 | Hinxton, UK | Decipher |  Helen Firth, DECIPHER consortium | Complete |
+| 7/1/2017 | Cedex, France | HPO-Opthalmology |   Panagiotis Sergouniotis, European Reference Network for Rare Eye Diseases | Complete |
+| 6/6/2024 | Istanbul | HPO-Affect (mood) workshop #1 |   | Complete |
+| 6/21/2024 | London | HPO GOSH event |   | Complete |
+| 6/19/2023 | Chicago | Mood disorder workshop #1 |   | Complete |
+| 6/1/2017 | Stanford, CA | HPO-Cardiology |  Matthew Wheeler | Complete |
+| 5/31/2024 | Online | Phenopackets Vulcan HL7 |   | Complete |
+| 5/1/2017 | Maryland | HPO-Immunology |  Morgan Similuk | Complete |
+| 4/6/2024 | Budapest | HPO-Affect (mood) workshop #2 |   | Complete |
+| 4/21/2015 | United Kingdom | NIHR RD-TRC |  Patrick Chinnery, Mareike Veltman and Roger James
+ | Complete |
+| 2019-2021 | Three workshops, numerous teleconferences, and joint task forces | Inborn errors of immunity (IEI) |  ESID (European Society for Immunodeficiencies) | Complete |
+| 2017-2024 |  | Nephrology (see PMID:32939051 ) |  Kidney Precision Medicine Project (KPMP) | Complete |
+| 2017-2023 | numerous teleconferences | Pulmonology (See PMID:36588100) |  ChILD EU, Matthias Griese | Complete |
+| 2017 | numerous teleconferences | Newborn screening (See PMID:33264411) |  Newborn Screening Translational Research Network (NBSTRN), Amy Brower | Complete |
+| 2/1/2023 | NIMH | Neurodevelopment and behavior |   | Complete |
+| 12/12/2013 | Unknown | HPO-Epilepsy |   Prof. Ingo Helbig | Complete |
+| 11/10/2024 | Farmington, CT | Lymphoma |   | Complete |
+| 10/20/2016 | Unknown | HPO-Bleeding |  BRIDGE BPD Consortium, Prof. Willem Ouwehand, University of Cambridge | Complete |
+| 10/13/2023 | Montreal | Mood disorder workshop #2 |   | Complete |
+|  |  | Contractures |   | Complete |
diff --git a/src/ontology/build-without-imports.sh b/src/ontology/build-without-imports.sh
@@ -11,3 +11,6 @@ test -f tmp/hpo-annotation-data/README.md
 ODK_TAG=$ODK sh run.sh make MIR=false IMP=false prepare_release -B
 ODK_TAG=$ODK sh run.sh make hpoa -B
 ODK_TAG=$ODK sh run.sh make hpo_diff -B
+
+# Update dynamically generated documentation pages
+ODK_TAG=$ODK sh run.sh make ../../docs/community/workshops.md -B
diff --git a/src/ontology/config/workshops.md.jinja2 b/src/ontology/config/workshops.md.jinja2
@@ -0,0 +1,7 @@
+# Workshop List
+
+| Date | Location | Topic | Coordination | Status |
+| ---- | -------- | ----- | ------------ | ------ |
+{%- for item in workshops | sort(attribute='When', reverse=true) %}{% if 'Complete' in item.Status %}
+| {{ item.When }} | {{ item.Where }} | {{ item.Topic }} | {% if item.Coordination is defined %} {{ item.Coordination }} {% endif %}| {{ item.Status }} |{% endif %}
+{%- endfor %}
diff --git a/src/ontology/hp.Makefile b/src/ontology/hp.Makefile
@@ -530,6 +530,14 @@ public_release:
 	gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes
 
 
+tmp/workshops.csv:
+	wget "https://docs.google.com/spreadsheets/d/e/2PACX-1vQT1u_xxXqS0rHR2lAF0NmdGHEaOuCFV3XDYPmdMldelAGmpUQSGTlU93bGvCSHDWDFRkzjq4vYe609/pub?gid=1737274956&single=true&output=csv" -O $@
+
+../../docs/community/workshops.md: tmp/workshops.csv config/workshops.md.jinja2
+	pip install jinjanator #Needed after/with ODK 1.5.3 --break-system-packages
+	python3 -c "import csv, json, sys; print(json.dumps({'workshops': list(csv.DictReader(open('$<')))}))" > tmp/workshops.json
+	jinjanate config/workshops.md.jinja2 tmp/workshops.json > $@
+
 #############################
 #### Adopt MP EQs ###########
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