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initial documentation for the metadata schema #5

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Sep 22, 2023
Merged

initial documentation for the metadata schema #5

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925ca3e
initial documentation for the metadata schema
mauerk Aug 3, 2023
972fa6e
updated template files
mauerk Aug 3, 2023
81e5419
Revert "updated template files"
mauerk Aug 3, 2023
c6c5c84
Rename docs folder
lkuchenb Aug 3, 2023
ef6e3d5
Template Update
lkuchenb Aug 3, 2023
1caa5ee
Remove README CI
lkuchenb Aug 3, 2023
4e59c2b
updated mkdocs to include data dictionary files
mauerk Aug 3, 2023
951ec11
Merge remote-tracking branch 'origin/main' into initial_doc_commit
lkuchenb Sep 20, 2023
d338840
Re-add overview
lkuchenb Sep 20, 2023
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12 changes: 11 additions & 1 deletion mkdocs.yaml
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Expand Up @@ -21,7 +21,7 @@ site_name: GHGA User Documentation
site_description: Public documentation of the German Human Genome-Phenome Archive.
site_author: The GHGA Team
site_url: https://docs.ghga-dev.de

docs_dir: user_docs
# Repository
repo_name: GHGA User Documentation
repo_url: https://github.com/ghga-de/docs/
Expand Down Expand Up @@ -82,9 +82,19 @@ nav:
- "Overview": index.md
- "GHGA Metadata Model":
- "Overview": metadata/overview.md
- "Standards": metadata/standards.md
- metadata/concepts.md
- metadata/modules.md
- "Entities & Attributes": metadata/entities.md
- "Data Dictionary":
- "Analysis Module": metadata/data_dictionary/analysis-module.md
- "Basic Module": metadata/data_dictionary/basic-module.md
- "Data Use Conditions Module": metadata/data_dictionary/data-use-conditions-module.md
- "Dataset Module": metadata/data_dictionary/dataset-module.md
- "Phenotype Module": metadata/data_dictionary/phenotype-module.md
- "Sample Module": metadata/data_dictionary/sample-module.md
- "Sequencing Module": metadata/data_dictionary/sequencing-module.md
- "File Submission": metadata/data_dictionary/file-submission.md
- "Tools":
- "GHGA Validator": validator/validator.md
- "GHGA Transpiler": transpiler/transpiler.md
47 changes: 47 additions & 0 deletions readme_generation.md
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<!--
Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
for the German Human Genome-Phenome Archive (GHGA)

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

-->

# Readme Generation

The README file is generated by collecting information from different sources as
outlined in the following.

- name: The full name of the package is derived from the remote origin Git repository.
- title: A title case representation of the name.
- shortname: An abbreviation of the full name. This is derived from the name mentioned
in the [`./setup.cfg`](`./setup.cfg).
- summary: A short 1-2 sentence summary derived from the description in the
[`./setup.cfg`](`./setup.cfg).
- version: The package version derived from the version specified in the
[`./setup.cfg`](`./setup.cfg).
- description: A markdown-formatted description of the features and use cases of this
service or package. Obtained from the [`./.description.md`](./.description.md).
- design_description: A markdown-formatted description of the overall architecture and
design of the package. Obtained from the [`./.design.md`](./.design.md).
- config_description: A markdown-formatted description of all config parameters.
This is autogenerated from the [`./config_schema.json`](./config_schema.json).
- openapi_doc: A markdown-formatted description of the HTTP API. This is autogenerated
and links to the [`./openapi.yaml`](./openapi.yaml). If the openapi.yaml is not
this documentation is empty.

The [`./.readme_template.md`](./.readme_template.md) serves as a template where the
above variable can be filled in using Pythons `string.Template` utility from the
standard library.

The [`./scripts/update_readme.py`] script can be used to collect all information and
fill it into the template to generate the README file.
17 changes: 17 additions & 0 deletions scripts/__init__.py
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# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
# for the German Human Genome-Phenome Archive (GHGA)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

"""Scripts and utils used during development or in CI pipelines."""
51 changes: 51 additions & 0 deletions scripts/update_all.py
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#!/usr/bin/env python3

# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
# for the German Human Genome-Phenome Archive (GHGA)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

"""Run all update scripts that are present in the repository in the correct order"""

try:
from scripts.update_template_files import main as update_template
except ImportError:
pass
else:
print("Pulling in updates from template repository")
update_template()

try:
from scripts.update_config_docs import main as update_config
except ImportError:
pass
else:
print("Updating config docs")
update_config()

try:
from scripts.update_openapi_docs import main as update_openapi
except ImportError:
pass
else:
print("Updating OpenAPI docs")
update_openapi()

try:
from scripts.update_readme import main as update_readme
except ImportError:
pass
else:
print("Updating README")
update_readme()
53 changes: 53 additions & 0 deletions user_docs/metadata/data_dictionary/analysis-module.md
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# **Analysis Module**

The **Analysis Module** captures the following entities and properties:

- Analysis
- title
- description
- [type](#type)
- [reference genome](#reference-genome)
- reference chromosome
- Analysis Process

## **Analysis**

### **type**
| Controlled Vocabulary | Ontology Term | Description |
| :-------------------- | :-----------: | :---------- |
| BAM | | |
| VCF | | |
| SAM/CRAM | | |

### **reference genome**
| Controlled Vocabulary | Ontology Term | Description |
| :-------------------- | :-----------: | :---------- |
| GRCh37 | | |
| GRCh37.p1 | | |
| GRCh37.p2 | | |
| GRCh37.p3 | | |
| GRCh37.p4 | | |
| GRCh37.p5 | | |
| GRCh37.p6 | | |
| GRCh37.p7 | | |
| GRCh37.p8 | | |
| GRCh37.p9 | | |
| GRCh37.p10 | | |
| GRCh37.p11 | | |
| GRCh37.p12 | | |
| GRCh37.p13 | | |
| GRCh38 | | |
| GRCh38.p1 | | |
| GRCh38.p2 | | |
| GRCh38.p3 | | |
| GRCh38.p4 | | |
| GRCh38.p5 | | |
| GRCh38.p6 | | |
| GRCh38.p7 | | |
| GRCh38.p8 | | |
| GRCh38.p9 | | |
| GRCh38.p10 | | |
| GRCh38.p11 | | |
| GRCh38.p12 | | |
| GRCh38.p13 | | |
| GRCh38.p14 | | |
40 changes: 40 additions & 0 deletions user_docs/metadata/data_dictionary/basic-module.md
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# **Basic Module**

The **Basic Module** captures the following entities and properties:

- Study
- title
- [type](#type)
- description
- affiliations
- Publication
- abstract
- author
- doi
- journal
- title
- xref
- year


## **Study**
### **type**

| Controlled Vocabulary | Ontology Term | Description |
| :---------------------- | :--------------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Cancer Genomics | [topic:0622] | Study of cancer genomics |
| Epigenetics | [topic:3295] | Study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence |
| Exome Sequencing | [EFO:0005396] | Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). Exons (the subset of DNA that encodes proteins) are selected, and the exonic DNA is then sequenced using any high-throughput DNA sequencing technology |
| Forensic Genomics | [OMIT:0025593] | Genetic samples to help identify crime victims, perpetrators, or family relationships |
| Paleo-genomics | [topic:3943] | The reconstruction and analysis of genomic information in extinct species |
| Gene Regulation Study | [topic:0204] | The regulation of gene expression |
| Metagenomics | [topic:3174] | The study of genetic material recovered from environmental samples, and associated environmental data |
| Other | | |
| Pooled Clone Sequencing | [EFO:0003741] | An assay in which DNA is the input molecule derived from pooled clones (for example BACs and Fosmids) is sequenced using high throughput technology using shotgun methodology |
| Population Genomics | [topic:3796] | Large-scale study (typically comparison) of DNA sequences of populations |
| RNASeq | [EFO:0008896] | A method that involves purifying RNA and making cDNA, followed by high-throughput sequencing |
| Resequencing | [operation:3923] | Laboratory experiment to identify the differences between a specific genome (of an individual) and a reference genome (developed typically from many thousands of individuals). WGS re-sequencing is used as golden standard to detect variations compared to a given reference genome, including small variants (SNP and InDels) as well as larger genome re-organisations (CNVs, translocations, etc.). ows re-sequencing of complete genomes of any given organism with high resolution and high accuracy |
| Synthetic Genomics | [topic:0622] | Sequencing of modified, synthetic, or transplanted genomes |
| Transcriptome Analysis | [EFO:0009865] | Sequencing and characterization of transcription elements |
| Whole Genome Sequencing | [topic:3673] | Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time |
| GWAS | [topic:3517] | Genome-wide association study experiments |
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