diff --git a/docs/community/index.md b/docs/community/index.md
index ca5b1897e..f0ac79f62 100644
--- a/docs/community/index.md
+++ b/docs/community/index.md
@@ -1,6 +1,6 @@
# HPO Community
-The HPO has been a community project since its inception in 2008. We are indebtled to all those who have made contributions of new terms, annotations, and other improvements. See the [Community page](https://hpo.jax.org/app/community){:target="_blank"} for more information.
+The HPO has been a community project since its inception in 2008. We are indebted to all those who have made contributions of new terms, annotations, and other improvements. See the [Community page](https://hpo.jax.org/app/community){:target="_blank"} for more information.
# Monarch Initiative
diff --git a/docs/css/custom.css b/docs/css/custom.css
new file mode 100644
index 000000000..e07644eb2
--- /dev/null
+++ b/docs/css/custom.css
@@ -0,0 +1,63 @@
+.legend {
+ margin-top: 1em;
+ padding: 0.5em;
+ background-color: #f9f9f9;
+ border-left: 4px solid #007acc;
+ font-style: italic;
+ }
+
+/* Target the table with the specific class (if using one) */
+.alt-rows-table {
+ width: 100%;
+ border-collapse: collapse;
+ }
+
+ /* Style for table rows */
+ .alt-rows-table tr:nth-child(odd) {
+ background-color: #f2f2f2; /* Light gray for odd rows */
+ }
+
+ .alt-rows-table tr:nth-child(even) {
+ background-color: #ffffff; /* White for even rows */
+ }
+
+ /* Style for the header row */
+ .alt-rows-table th {
+ background-color: #4CAF50; /* Change to your desired color (e.g., green) */
+ color: white; /* White text for contrast */
+ text-align: left;
+ padding: 8px 12px;
+ }
+
+ /* Optional: Add borders and padding to make the table more readable */
+ .alt-rows-table th, .alt-rows-table td {
+ padding: 8px 12px;
+ border: 1px solid #ddd;
+ }
+
+/* Optional: Add borders and padding to make the table more readable */
+.alt-rows-table th, .alt-rows-table td {
+ padding: 8px 12px;
+ border: 1px solid #ddd;
+ }
+
+.alt-rows-table th {
+ background-color: #4D4DFF; /* Light gray background for header */
+ text-align: left;
+}
+
+figure .left-align {
+ text-align: left;
+ margin-top: 8px; /* Optional: Adjust spacing above the caption */
+}
+
+/* Highlight box for important sentences */
+.highlight-box {
+ border: 2px solid #4CAF50; /* Green border */
+ background-color: #f9f9f9; /* Light gray background */
+ padding: 12px;
+ border-radius: 5px; /* Rounded corners */
+ font-size: 1rem;
+ color: #333; /* Dark text */
+ margin: 10px 0; /* Spacing around the box */
+}
diff --git a/docs/img/depressedmood.png b/docs/img/depressedmood.png
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diff --git a/docs/index.md b/docs/index.md
index 641602e0d..e96458540 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -5,16 +5,16 @@ It provides a structured representation of abnormal characteristics associated w
HPO helps researchers and clinicians share and integrate phenotypic data, making understanding and diagnosing genetic disorders easier.
It uses a hierarchical organization and semantic relationships between terms and allows for annotation of genes and diseases. HPO is used in multiple diagnosis and variant prioritization tools, aiding healthcare professionals and researchers in identifying and classifying genetic conditions.
In 2023, HPO released an international edition which covers different languages such as Chinese, Turkish, Japanese, Spanish and Czech ([more](https://obophenotype.github.io/hpo-translations/)).
-The translations are displayed in the various browsers (e.g. [HPO App](https://hpo.jax.org/app/browse/term/HP:0001166) and [OLS](https://www.ebi.ac.uk/ols4/ontologies/hp)).
+The translations are displayed in the various browsers (e.g. [HPO App](https://hpo.jax.org/app/browse/term/HP:0001166){:target="\_blank"} and [OLS](https://www.ebi.ac.uk/ols4/ontologies/hp)){:target="\_blank"}.
-This site contains documentation for clinicians, researchers, developers, and other users of the [HPO](https://hpo.jax.org/app/).
+This site contains documentation for clinicians, researchers, developers, and other users of the [HPO](https://hpo.jax.org/app/){:target="\_blank"}.
### A snapshot of the HPO hierarchy
-
+{:target="\_blank"}
### The HPO App
-
+{:target="\_blank"}
To learn more, explore the [HPO app](https://hpo.jax.org/app/).
diff --git a/docs/workshops/annotations.md b/docs/workshops/annotations.md
new file mode 100644
index 000000000..b5cb876cc
--- /dev/null
+++ b/docs/workshops/annotations.md
@@ -0,0 +1,18 @@
+# Disease annotations
+
+The HPO team is transitioning to [GA4GH Phenopacket](https://phenopacket-schema.readthedocs.io/en/latest/){:target="\_blank"} format for annotating cases and diseases. We have created the
+[phenopacket store](https://github.com/monarch-initiative/phenopacket-store){:target="\_blank"} as a repository for individual-level information. We are working on the [pyphetools](https://monarch-initiative.github.io/pyphetools/){:target="\_blank"} package to streamline annotation of phenopackets.
+
+Our software for this application is in development. We will discuss current options during the workshop.
+
+
+## RareLink
+[RareLink](https://rarelink.readthedocs.io/en/latest/index.html){:target="\_blank"} is a new tool that enables efficient and accurate entry of HPO and other data related to rare disease medicine.
+
+[RareLink](https://rarelink.readthedocs.io/en/latest/index.html){:target="\_blank"} is a tool for managing and processing rare disease data within the REDCap. RareLink aims to maximise the utility of REDCap by providing a comprehensive framework designed specifically for rare disease (RD) research and care. RareLink streamlines import of tabular data (e.g., Excel, relational database).
+
+RareLink additionally provides a preconfigured data collection sheets based on the RD-CDM and user guides for manual data capture to ensure precision and correctness of data captured. Further, RareLink defines guidelines for developing more specialised REDCap sheets around the RD-CDM so that the data captured can also be processed by our framework to generate FHIR resources and Phenopackets.
+
+RareLink is designed to be deployed and installed in a local REDCap instance. Using the guidelines provided, or using our preconfigured RareLink-REDCap and setting up the RareLink API, you can ensure that the data captured is compliant with the our framework to generate FHIR resources and Phenopackets.
+
+We will typically provide a short introduction to RareLink at HPO workshops.
\ No newline at end of file
diff --git a/docs/workshops/good_structure.md b/docs/workshops/good_structure.md
new file mode 100644
index 000000000..4eefbebe3
--- /dev/null
+++ b/docs/workshops/good_structure.md
@@ -0,0 +1,142 @@
+# Rules For Good HPO Structure
+
+Creating a good HPO (see [here](good_term.md)) is not all we need to do. We also need to decide
+where to place the term in the HPO hierarchy. There are several rules of thumb that can help with this.
+
+
+## True-Path Rule
+The true path rule (also known as annotation propagation rule) states:
+
+ If a term can be used to describe a patient then all parents of that term can be used to describe that patient.
+
+
+
+
+{ width="600" }
+Iridescent posterior subcapsular cataract.
+Hierarchy for Iridescent posterior subcapsular cataract (HP:0007889).
+
+
+
+In this case, if a patient is diagnosed with
+[Iridescent posterior subcapsular cataract (HP:0007889)](https://hpo.jax.org/browse/term/HP:0007889){:target="\_blank"}, it is true that the patient can also be said to have [Posterior subcapsular cataract (HP:0007787)](https://hpo.jax.org/browse/term/HP:0007889){:target="\_blank"}, because every *Iridescent posterior subcapsular cataract* is also a *Posterior subcapsular cataract* (i.e., *Iridescent posterior subcapsular cataract* is a specific kind of *Posterior subcapsular cataract*).
+
+Similarly, the patient can be said to have a [Subcapsular cataract (HP:0000523)](https://hpo.jax.org/browse/term/HP:0000523) because every *Posterior subcapsular cataract* is also a *Subcapsular cataract*. The same thing is true of all of the ancesters, e.g., the patient can be said to have a
+[Cataract (HP:0000518)](https://hpo.jax.org/browse/term/HP:0000518){:target="\_blank"} and
+[Abnormal lens morphology (HP:0000517)](https://hpo.jax.org/browse/term/HP:0000517){:target="\_blank"} and so on up to the root of the ontology, [Phenotypic abnormality (HP:0000118)](https://hpo.jax.org/browse/term/HP:0000118){:target="\_blank"}.
+
+## When is the true-path rule violated?
+
+Consider the following example. Currently, in the HPO, [Cataract (HP:0000518)](https://hpo.jax.org/browse/term/HP:0000518){:target="\_blank"} is a subclass of
+[Abnormal lens morphology (HP:0000517)](https://hpo.jax.org/browse/term/HP:0000517){:target="\_blank"}. This is always true for reasons explained above. Let's say we decided to make
+[Cataract (HP:0000518)](https://hpo.jax.org/browse/term/HP:0000518){:target="\_blank"} also be a subclass of [Reduced visual acuity (HP:0007663)](https://hpo.jax.org/browse/term/HP:0007663){:target="\_blank"}
+because individuals with cataract tend to have vision problems.
+
+This would violate the true-path rule, because it is not true that all individuals with cataract have reduced visual acuity. Rarely, visual acuity can be normal with certain kinds of congenital cataract. However, HPO-based software uses the true-path rule to infer that if a patient is explicitly annotated to a certain term, the patient is implicitly annotated to all of the ancestors of the term, which would not always be true in this example.
+
+
+## Avoid bundled terms
+
+Avoid creating terms that refer to multiple phenotypes that do not easily fit under a broader term.
+
+For example, a concept such as "Bipolar disease I" is not a good HPO term because it is a diagnostic term that refers to an individual with a history of at least one manic episode who displays the following characteristics:
+
+
+
+
+
Label
+
Description
+
+
+
+
+
A
+
Distinct period of mood disturbance
+
+
+
B
+
Manic symptoms
+
+
+
C
+
Severe mood disturbance
+
+
+
D
+
Not attributable to a substance or other medical condition
+
+
+
+
+Table 1: Criteria for bipolar disease I.
+
+
+To specify a disease, it is preferable to use a term from a disease ontology such as Mondo.
+
+### Exceptions
+
+Many Mendelian diseases are characterized by a highly increased risk for certain diseases. For instance, individuals with Bardet-Biedl syndrome frequently have [Diabetes mellitus (HP:0000819)](https://hpo.jax.org/browse/term/HP:0000819){:target="\_blank"}. Frequently, this is the only information that is available in medical publications (e.g., it would be noted that a person with BBS has diabetes, but the manifestations and time course of diabetes in that individual are not specified). For this reason, the
+HPO has a number of "diagnostic" terms.
+
+Also, in some cases, a medical history of a disease can be considered to be a phenotypic feature. For instance, infections following live vaccinations such as [BCGosis HP:0020087](https://hpo.jax.org/browse/term/HP:0020087){:target="\_blank"} can be manifestations of some inborn errors of immunity.
+
+
+## Pie rule
+The Pie Rule (also known as the Brie rule) states:
+
+The set of child terms of a given term should robustly cover the specific subclasses of the parent term, such that a parent term could always be replaced with a more specific child term.
+
+
+
+{ width="200" }
+Pie rule.
+If a term has one or more subclasses, then ideally the subclasses should be about the same "size" and completely cover the pie.
+
+
+
+Consider, for instance, the term [Abnormal cardiac septum morphology (HP:0001671)](https://hpo.jax.org/browse/term/HP:0001671){:target="\_blank"}.
+
+
+{ width="300" }
+Abnormal cardiac septum morphology.
+
+
+
+Abnormal cardiac septum morphology has three subterms. On the HPO website, if you hover over the gray bars, you can see the number of descendent terms for each of them.
+
+- [Abnormal ventricular septum morphology (HP:0010438)](https://hpo.jax.org/browse/term/HP:0010438){:target="\_blank"}: 14 subterms, including specific terms such as [Perimembranous ventricular septal defect HP:0011682](https://hpo.jax.org/browse/term/HP:0011682){:target="\_blank"}.
+- [Abnormal atrial septum morphology (HP:0011994)](https://hpo.jax.org/browse/term/HP:0011994){:target="\_blank"}: 8 subterms, including specific terms such as [Secundum atrial septal defect (HP:0001684)](https://hpo.jax.org/browse/term/HP:0001684){:target="\_blank"}
+- [Atrioventricular canal defect (HP:0006695)](https://hpo.jax.org/browse/term/HP:0006695){:target="\_blank"}: 6 subterms, including specific terms such as [Complete atrioventricular canal defect (HP:0001674)](https://hpo.jax.org/browse/term/HP:0001674){:target="\_blank"}.
+
+
+Thus, here the HPO attempts to cover all of the specific kinds of *Abnormal cardiac septum morphology*.
+The three main subclasses are covered and all three have roughly the same number of terms. It would be a mistake, in contrast, if [Abnormal cardiac septum morphology (HP:0001671)](https://hpo.jax.org/browse/term/HP:0001671){:target="\_blank"} had the subclasses
+[Abnormal ventricular septum morphology (HP:0010438)](https://hpo.jax.org/browse/term/HP:0010438){:target="\_blank"}, [Abnormal atrial septum morphology (HP:0011994)](https://hpo.jax.org/browse/term/HP:0011994){:target="\_blank"}, and then [Complete atrioventricular canal defect (HP:0001674)](https://hpo.jax.org/browse/term/HP:0001674){:target="\_blank"}, [Partial atrioventricular canal defect (HP:0011577)](https://hpo.jax.org/browse/term/HP:0011577){:target="\_blank"}, and so on for the other four child terms of [Atrioventricular canal defect (HP:0006695)](https://hpo.jax.org/browse/term/HP:0006695){:target="\_blank"}, because the former two terms have a different granularity (they are grouping terms) than the latter (they are specific terms).
+
+## The 5 o-clock rule
+This rule states that
+
+Terms should be easy to find by walking down the hierarchy. That is, a clinician should be able to find the right term at 5:00 pm on a Friday after a long work week.
+
+
+It is of course hard to precisely define this rule, but basically the hierarchy of the HPO should reflect, to the extent possible, current clinical thinking and not ontological abstractions.
+
+
+# Why are these rules important?
+
+Consider the following (made-up) example. At first glance, it may appear correct - after all, patients with depressed mood may lose weight, be tearful, and have sleep disturbances.
+
+
+
+{ width="400" }
+Example: depressed mood.
+
+
+
+However, note that these are not actually **subclass** relations. Instead, they are **has-phenotype** relations in the sense that a patient with depressed mood often has the three phenotypic features in question. However, not every patient with sleep distrubance has depressed mood. Other causes include
+sleep apnea, restless Legs Syndrome, narcolepsy, chronic pain, certain medications, caffeine, alcohol, environmental factors such as loud noises, thyroid conditions, parkinson disease, and many others.
+
+Therefore, if we encoded this relation in the HPO (which only uses subclass relations), then HPO-aware computer programs would falsely conclude that every patient with any one of the above diseases who happened to have a sleep disturbance also has depressed mood. While this may be true for some, it is not true in general, and this would lead to erroneous results.
+
+The structure of the HPO is designed to follow the above rules to ensure accuracy of computational algorithms that use HPO.
+
diff --git a/docs/workshops/good_term.md b/docs/workshops/good_term.md
new file mode 100644
index 000000000..a5e9d1424
--- /dev/null
+++ b/docs/workshops/good_term.md
@@ -0,0 +1,116 @@
+# What is a Good HPO Term?
+
+
+## New term requests
+
+The simplest way to contribute to the HPO is to make a new term request on our [issue tracker](https://github.com/obophenotype/human-phenotype-ontology/issues){:target="\_blank"} on Github. The following text is intended to serve as a guide for anyone who would like to contribute to the HPO project by making new term requests.
+
+## Does the term you are looking for already exist?
+First, please look at the current HPO and check whether the term is already there. Use the browser on this website.
+
+## Is the term you are looking for a synonym of an existing term?
+If you do not immediately find the term you are looking for, please look for synonyms. One way of doing this is to go to a likely parent of the term and peruse all of the children to spot a likely synonym. For instance, if you are looking for a term entitled Defect in the atrial septum and do not find it, go to the term [Abnormal cardiac atrium morphology (HP:0005120)](https://hpo.jax.org/browse/term/HP:0005120){:target="\_blank"}. and look through all of the children. With some luck you will find the term
+[Atrial septal defect (HP:0001631)](https://hpo.jax.org/browse/term/HP:0001631){:target="\_blank"} and recognize that *Defect in the atrial septum* is listed as a synonym of [Atrial septal defect (HP:0001631)](https://hpo.jax.org/browse/term/HP:0001631){:target="\_blank"}.
+
+## Bundled terms
+If you find a description in a publication such as "Sparse eyebrows and eyelashes", note that the description is referring to two separate phenotypic features. The HPO would encode this using two different terms, [Sparse eyebrow (HP:0045075)](https://hpo.jax.org/browse/term/HP:0045075){:target="\_blank"} and
+[Sparse eyelashes (HP:0000653)](https://hpo.jax.org/browse/term/HP:0000653){:target="\_blank"}. The idea is that one HPO term should refer to an atomic phenotypic abnormality rather than to a collection of abnormalities observed in an individual patient. Please debundle the description and proceed as described above. This is a central tenet of Deep phenotyping.
+
+## Anatomy of a good term suggestion
+A good term request provides the information shown in Table 1. Please use our GitHub issue tracker, choosing the “New Term” template.
+
+
+
+
Item
+
Example
+
+
+
+
+
Disease ID
+
OMIM:265380
+
+
+
Disease Name
+
Alveolar capillary dysplasia with misalignment of pulmonary veins
+
+
+
HPO ID
+
HP:0001734
+
+
+
HPO Term Name
+
Annular pancreas
+
+
+
Frequency
+
2/14
+
+
+
Onset
+
Congenital onset (use terms from the HPO Onset hierarchy)
+
+
+
PMID
+
PMID:19500772
+
+
+
Comment
+
Any other information or context
+
+
+
+
+Table 1: Components of a complete and well-structured new term request.
+
+
+## How to suggest new disease annotations
+We welcome suggestions for novel disease annotations (HPOAs) to add to HPO. These can be made by submitting a ticket to the HPO tracker with the information shown in Table 2. Please use our GitHub issue tracker, choosing the “New Annotation” template.
+
+
+
+
+
+
Item
+
Example
+
+
+
+
+
Disease ID
+
OMIM:265380
+
+
+
Disease Name
+
Alveolar capillary dysplasia with misalignment of pulmonary veins
+
+
+
HPO ID
+
HP:0001734
+
+
+
HPO Term Name
+
Annular pancreas
+
+
+
Frequency
+
2/14
+
+
+
Onset
+
Congenital onset (use terms from the HPO Onset hierarchy)
+
+
+
PMID
+
PMID:19500772
+
+
+
Comment
+
Any other information or context
+
+
+
+
+Table 2: Components of a complete and well-structured new disease annotation request.
+
+
diff --git a/docs/workshops/index.md b/docs/workshops/index.md
new file mode 100644
index 000000000..eef2d0094
--- /dev/null
+++ b/docs/workshops/index.md
@@ -0,0 +1,16 @@
+# HPO Workshops
+
+
+The HPO has been a community project since its inception in 2008. We are indebted to all those who have made contributions of new terms, annotations, and other improvements. See the [Community page](https://hpo.jax.org/app/community){:target="_blank"} for more information.
+
+There are many ways of contributing to the HPO project. One of the most important consists of community workshops, in which experts in a certain medical domain come together to review, revise, and extend specific areas of the HPO such as ophthalmology, mental disease, or immunology.
+
+
+
+
+## Topics
+
+- [What is a good HPO term?](good_term.md)
+- [Rules For Good HPO Structure](good_structure.md)
+- [What is the difference between a disease and a phenotypic feature?](../documentation/clinicians.md)
+- [Previous workshops](../community/workshops.md)
\ No newline at end of file
diff --git a/docs/workshops/practical.md b/docs/workshops/practical.md
new file mode 100644
index 000000000..b987be825
--- /dev/null
+++ b/docs/workshops/practical.md
@@ -0,0 +1,78 @@
+# Workshop procedure
+
+Each HPO workshop is a little different, but in general, we plan for one or two days. Usually, the schedule of a workshop resembles the following plan.
+
+1. Lecture. Review of the HPO project and its applications in genomic diagnostics and translational research. (60 min)
+2. Review of the rules for making new HPO terms (see the other pages in this section). (30min)
+3. Discussion and demonstration of tools for the workshop. Depending on the setting, we have used Google spreadsheets, online forms (airtable), or pencil and paper to capture the suggestions of workshop participants. This is because different projects and different groups are at different stages and have distinct goals.
+4. Group session. We typically start with a session involving the entire group in which we review a small section of the HPO and create 3-5 terms together, so that participants gain confidence in working with the HPO.
+5. Breakout sessions. We typically ask groups to identify subtopics for smaller breakout groups (of 3-10 members). These groups will review the relevant part of the HPO in depth, creating new terms, revising and improving existing terms and structure.
+6. Report-back. The breakout groups report to the group as a whole, and if necessary, revisit the terms created in the breakouts according to suggestions of the group.
+7. Hand-off. The breakout groups usually define a group leader who coordinates the remaining work with the HPO team. For instance, the HPO term will plan to add the new terms to the official HPO files using either scripts or adding some terms manually using tools such as Protege.
+
+# Getting started
+
+In our experience, it takes first-time participants a few hours to get the hang of things. This is OK, and the HPO project is insensely grateful to its many contributors for taking the time to help us improve the resource -- we will take enough time during the workshops to discuss questions and doubts.
+
+This section provides an example of the kind of work you will be doing.
+
+
+
+
+{ width="1000" }
+Esophageal atresia.
+Hierarchy for Iridescent posterior subcapsular cataract (HP:0007889).
+
+
+
+At the time of this writing (Nov. 24, 2024), the term [Esophageal atresia (HP:0002032)](https://hpo.jax.org/browse/term/HP:0002032){:target="\_blank"} has only one child term, [Proximal esophageal atresia (HP:0004403)](https://hpo.jax.org/browse/term/HP:0004403){:target="\_blank"}. The latter term has no definition, no citation to an article in PubMed, and no synonyms. Therefore, several rules described in the sections on [good HPO structure](good_structure.md) and [good HPO term content](good_term.md) are violated, and so there is ample opportunity to improve this part of the HPO.
+
+When you are considering whether a term needs work, reflect on the following issues.
+
+
+
+
Do the children of the term include all relevant concepts? Is the granularity of the child terms similar? (Pie rule)
+
Do you need to create a new term? (also Pie rule)
+
Is the structure (or relationships between terms) correct? (True path rule)
+
Do you need to add more synonyms?
+
Could the label or definition of a term use some added clarification? (5 o'clock rule)
+
+
+
+In this case, here are some of the things we could do.
+
+## Add a definition
+
+We can search in PubMed using a search term such as "esophageal atresia"[title]. If we search in Google, it is good to search on "esophageal atresia" AND PMID in order to find an article listed in PubMed which we can cite in the HPO.
+
+One of the articles that this search turned up was [Sfeir R, et al. (2013) Epidemiology of esophageal atresia. Dis Esophagus 26(4):354-5](https://pubmed.ncbi.nlm.nih.gov/23679022/){:target="\_blank"}. We can extract the first two sentence from the abstract of this article for our definition:
+
+
+Esophageal atresia (EA) is a rare congenital malformation consisting of a lack of continuity between the upper and lower esophageal pouches, frequently associated with tracheoesophageal fistula.
+
+
+It is acceptable to use large-language models as a part of the search process, but we ask that all definitions are derived from a citable source and that a human expert has vetted the source and the definition.
+
+# Add synonyms
+
+Synonyms are useful because they help users more easily find HPO terms and they are also used by most text-mining tools that identify HPO terms in texts. This is an application where LLMs can be very useful if the answers are checked by an expert. In this case, GPT suggested "Esophageal agenesis", which is not a synonym (agenesis means complete absence, while atresia means that the esophagus ends in a blind pouch instead of connecting to the stomach). However, "Esophagus atresia" is correct.
+
+# Add related terms
+
+We may decide to add more child terms to [Esophageal atresia (HP:0002032)](https://hpo.jax.org/browse/term/HP:0002032){:target="\_blank"}. It is often good to search for information about classifications of defects or abnormalities. In this case, we find a review article on the anomaly: [Spitz L (2007) Oesophageal atresia. Orphanet J Rare Dis. 2:24](https://pubmed.ncbi.nlm.nih.gov/17498283/){:target="\_blank"}.
+
+In our workshops, often participants will be aware of the classifications most used in their field and are able to specify the key citations. We ask participants to prepare themselves for our workshop by identifying analogous classifications in their field that are relevant for the topics to be worked on.
+
+Here, we see that there are several common anatomical types of oesophageal atresia.
+
+- Esophageal atresia with distal tracheooesophageal fistula
+- Esophageal atresia without tracheooesophageal fistula
+- H-type tracheooesophageal fistula (4%)
+
+The first category is the most common variety in which the proximal oesophagus, which is dilated, and the muscular wall thickened ends blindly in the superior mediastinum at about the level of the third or fourth thoracic vertebra. We may need to relabel this terms to reflect this, i.e., to change the label of
+[Proximal esophageal atresia (HP:0004403)](https://hpo.jax.org/browse/term/HP:0004403){:target="\_blank"} to *Esophageal atresia with distal tracheooesophageal fistula*. If we are not sure if these are refering to the same medical entity, we would leave the original term and add a corresponding definition.
+Typically, there is group discussion about such issues.
+
+# Disease annotations
+
+Ideally, we would also collect information about case or cohort reports that describe Mendelian diseases that can be characterized by Esophageal atresia. We can start by looking at the Disease annotations tab of the correpsonding page on the HPO website: [Esophageal atresia (HP:0002032)](https://hpo.jax.org/browse/term/HP:0002032){:target="\_blank"}. If we know of a disease that has this association but is not listed there, we can add the information by creating an issue on the GitHub tracker or directly during the workshop.
\ No newline at end of file
diff --git a/mkdocs.yaml b/mkdocs.yaml
index 9f78b7661..90f85d1ae 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -39,6 +39,9 @@ markdown_extensions:
site_url: https://obophenotype.github.io/human-phenotype-ontology/
repo_url: https://github.com/obophenotype/human-phenotype-ontology/
+extra_css:
+ - css/custom.css
+
nav:
- Home: index.md
- Documentation:
@@ -81,4 +84,10 @@ nav:
- Workshops: community/workshops.md
- Cite the HPO: community/cite.md
- HPO Internationalization Effort: https://obophenotype.github.io/hpo-translations/
+ - Workshops:
+ - Introduction: workshops/index.md
+ - What is a good HPO term?: workshops/good_term.md
+ - Rules For Good HPO Structure: workshops/good_structure.md
+ - Disease annotations: workshops/annotations.md
+ - Workshop procedure: workshops/practical.md