From c09299ba02ad35bd020768d84ff7d40299a40c13 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 3 Nov 2024 02:06:49 +0200 Subject: [PATCH] update linkml docs index page (#396) --- src/doc-templates/index.md.jinja2 | 105 +++++++++++++++++++++++------- 1 file changed, 81 insertions(+), 24 deletions(-) diff --git a/src/doc-templates/index.md.jinja2 b/src/doc-templates/index.md.jinja2 index 2a78e4c4..c6fd8704 100644 --- a/src/doc-templates/index.md.jinja2 +++ b/src/doc-templates/index.md.jinja2 @@ -1,21 +1,94 @@ -# {% if schema.title %}{{ schema.title }}{% else %}{{ schema.name }}{% endif %} +# SSSOM Official Data Model Documentation + +![SSSOM banner](images/sssom-banner.png) {% if schema.description %}{{ schema.description }}{% endif %} -URI: {{ schema.id }} +**Schema PURL**: {{ schema.id }} + +## Introduction + +While the SSSOM model is quite general and mappings can be shared in different formats, the most common format is the [SSSOM/TSV format](spec-formats-tsv.md). +Here is a tabular representation of some example mappings for illustration purposes: + +| subject_id | subject_label | predicate_id | object_id | object_label | mapping_justification | author_id | confidence | comment | +|---------------|---------------|-----------------|-----------------|----------------------|-----------------------------|-------------------------|------------|---------------------------------------------------------------------------------------------------------------------------------| +| KF_FOOD:F001 | apple | skos:exactMatch | FOODON:00002473 | apple (whole) | semapv:ManualMappingCuration | orcid:0000-0002-7356-1779 | 0.95 | "We could map to FOODON:03310788 instead to cover sliced apples, but only 'whole' apple types exist." | +| KF_FOOD:F002 | gala | skos:exactMatch | FOODON:00003348 | Gala apple (whole) | semapv:ManualMappingCuration | orcid:0000-0002-7356-1779 | 1.0 | | +| KF_FOOD:F003 | pink | skos:exactMatch | FOODON:00004186 | Pink apple (whole) | semapv:ManualMappingCuration | orcid:0000-0002-7356-1779 | 0.9 | "We could map to FOODON:00004187 instead which more specifically refers to 'raw' Pink apples. Decided against to be consistent with other mapping choices." | +| KF_FOOD:F004 | braeburn | skos:broadMatch | FOODON:00002473 | apple (whole) | semapv:ManualMappingCuration | orcid:0000-0002-7356-1779 | 1.0 | | + +In the TSV format, mapping set metadata is included at the top of the file, before the mappings themselves, in yaml-like key-value pairs: + + +!!! info "Example header (YAML format)" + + 
+    curie_map:
+      FOODON: http://purl.obolibrary.org/obo/FOODON_
+      KF_FOOD: https://kewl-foodie.inc/food/
+      orcid: https://orcid.org/
+    mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
+    mapping_set_description: >
+      Manually curated alignment of KEWL FOODIE INC internal food and 
+      nutrition database with Food Ontology (FOODON). Intended to be 
+      used for ontological analysis and grouping of KEWL FOODIE INC 
+      related data.
+    license: https://creativecommons.org/licenses/by/4.0/
+    mapping_date: 2022-05-02
+
+ +See [here](https://github.com/mapping-commons/sssom/tree/master/examples/schema) for concrete examples. -Name: {{ schema.name }} -{% if include_top_level_diagram %} +## Mapping metadata elements +{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%} +{% if c.name == "mapping" %} +{{gen.link(c)}}: {{c.description|enshorten}} + +| Column/Field | Description | Required | +|--------------------|---------------------------------------------------------|-------------| +{%- for slot in c.slots %} +{%- set slot_info = schemaview.get_slot(slot) %} +| **{{ gen.link(slot) }}** | {{ slot_info.description | default("No description") }} | {% if slot_info.required | default(false) %}Required{% elif slot_info.recommended | default(false) %}Recommended{% else %}Optional{% endif %} | +{%- endfor %} +{%- endif %} +{%- endfor %} + +## Mappings set metadata elements + +{% for c in gen.all_class_objects()|sort(attribute=sort_by) -%} +{% if c.name == "mapping set" %} +{{gen.link(c)}}: {{c.description|enshorten}} + +| Column/Field | Description | Required | +|--------------------|---------------------------------------------------------|-------------| +{%- for slot in c.slots %} +{%- set slot_info = schemaview.get_slot(slot) %} +| **{{ gen.link(slot) }}** | {{ slot_info.description | default("No description") }} | {% if slot_info.required | default(false) %}Required{% elif slot_info.recommended | default(false) %}Recommended{% else %}Optional{% endif %} | +{%- endfor %} +{%- endif %} +{%- endfor %} + +{# ## Schema Diagram ```{{ gen.mermaid_directive() }} {{ gen.mermaid_diagram() }} ``` -{% endif %} +#} +## Index (all classes, enums and elements) -## Classes +### Columns/Slots/Fields + +| Slot | Description | +| --- | --- | +{% for s in gen.all_slot_objects()|sort(attribute=sort_by) -%} +| {{gen.link(s)}} | {{s.description|enshorten}} | +{% endfor %} + +### Classes | Class | Description | | --- | --- | @@ -29,15 +102,7 @@ Name: {{ schema.name }} {% endfor %} {% endif %} -## Slots - -| Slot | Description | -| --- | --- | -{% for s in gen.all_slot_objects()|sort(attribute=sort_by) -%} -| {{gen.link(s)}} | {{s.description|enshorten}} | -{% endfor %} - -## Enumerations +### Enumerations | Enumeration | Description | | --- | --- | @@ -45,18 +110,10 @@ Name: {{ schema.name }} | {{gen.link(e)}} | {{e.description|enshorten}} | {% endfor %} -## Types +### Types | Type | Description | | --- | --- | {% for t in gen.all_type_objects()|sort(attribute=sort_by) -%} | {{gen.link(t)}} | {{t.description|enshorten}} | {% endfor %} - -## Subsets - -| Subset | Description | -| --- | --- | -{% for ss in schemaview.all_subsets().values()|sort(attribute='name') -%} -| {{gen.link(ss)}} | {{ss.description|enshorten}} | -{% endfor %}