v0.10.0 (#46)

* Proposed tweaks to speed up ds-graph performance (#36)

* Proposed tweaks to speed up ds-graph performance

* Stop using owl.template in donor.yaml

* Remove "links back to" relationship

* Remove "partially overlaps" relationship

* Simplify the "sex_id" and "race_id" annotations

* Remove the redundant extraction_site relationship

This relationship is already handled by the rui_location (or formally it is defined as "has_registration_location").

* Add metadata module to generate the ontology metadata

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Co-authored-by: Josef Hardi <[email protected]>

* Improve error handling to help on debugging

* Fix when a sample block has no registration location

For example, samples from CellxGene repository

* Commit the sssom schema

* Convert the attributes to first class slots

* Removing 'equals_string' expression due to known LinkML bug

Refer to linkml/linkml#1855 ticket to learn more about the bug.

* Improve execution logging to debug better

* Remove unnecessary prefixes

* Explicitly declare slot_uri and class_uri to avoid mix-ups during OWL generation.

* Fix info logging should use the name variable

* Exclude Eukaryota organism hierarchy

* Remove unused variables

* Fix typo

Thanks to Andi who pointed this out.

* Commit schema for ctann DO

* Initial commit for ctann data normalization

* Initial commit for CTAnn data enrichment.

* Update LinkML versions

* Replace with full IRI

* Added references as part of dataset metadata

* Write a module to extract DOI and BioRxiv references from text

* Implement reference extraction from description text in metadata normalization

* Include references mentioned explicitly in the metadata.yaml file

* Set www. as optional in the regex

* Add references field to README.md and index.html files

* Align donor schema with raw data schema.

* Rename external_link to link per raw schema

* Explicitly mention slot_uri

* Remove collision summaries and corridors as they belong to spatial entities

* Remove unused class and slot

* Add collision summaries, corridor, and cell summaries to spatial entity

* Rename external_link to link per raw data schema

* Rename cell_summaries to summaries per raw data schema

* Add cell_count, gene_count and organ_id to dataset schema

* Remove unused argument

* Explicitly mention slot_uri on each slot

* Rename file_url to file per raw data schema

* Set corridor's parent to spatialEntity, not tissue block

* Rename collision_items to collisions per raw data schema

* Refactor code

* Rename slots to align with the raw data schema

* Rename slots to align with raw data schema

* Explicitly mention slot_uri on each slot

* Ensure a consistent definition of percentage

* Fix missing aggregated_summary_count and aggregated_summaries

* Fix argument name

* Updated top-level attribute names for uniqueness and to prevent collisions with existing attributes

* Fix missing spatialEntity reference

* Make collisions as optional

* Expand any compact ASCTB-TEMP terms to its full IRI

* Remove ASCTB-TEMP prefix to prevent automatic IRI compaction by CLI tool

The ASCTB-TEMP prefix was causing the expanded IRI to be automatically compacted by the command line tool, resulting in invalid compacted names (e.g., ASCTB-TEMP:-cells-ins-). This could lead to parsing errors when the tool encounters these improperly formatted names.

* Explicitly append CCF prefix to entity type names to ensure correct IRI generation

* Add testing framework for evaluating enriched graph data

* Rename test to validate

* Normalize the aggregated cell summaries

* More on renaming slots to align with the raw data

* Use EntityID to simplify the slot definition

* Fix description

* Fix the schema to support sample comes_from donor relationship

* Updating test case queries

* Add Sample class for backward compatibility

* Add a new sample_type slot

* Rename slot

* Map description slot to rdfs:comment

* Swap values between rdfs:label and skos:prefLabel

* Update the query to find tissue blocks and tissue sections

* Add references in the dataset object

* Map to its original slot name

* Update the test query to if references exists

* Fix the missing pref_label property

* Return error log excluding the long message field

* Add anatomical structure collision object to schema

* Update cell summary data to use blank nodes

* Update collision data to use blank nodes

* Update collision data to use blank nodes

* Add creator first and last name properties

* Fix date off by one day

* Suppress warning messages

* Updating the number types

* Suppress log messages from mmdc command

* Remove unused slots

* Move spatial placement into its own record in the model

* Adjust enrichment logic to reflect recent model changes

* Patch ds-graph context to include @reverse property support

* Create utility script for converting YAML into JSON-LD format

* Update SPARQL test cases to ensure accurate query validation

* Disambiguate dataset entities: use Dataset to refer to experimental dataset and RawDataset for source input for creating a DO graph

* Skip date processing when format is already YYYY-MM-DD

* Update test cases to handle regular ds-graph structure (non hra-pop)

* Add usage comments

* Set range as reference ID to actual entities

* Get rid of settings

* Improve code to normalize various date formats to YYYY-MM-DD format

* Enable normalization and enrichment of ds-graph data

* Update requirements-freeze.txt

* Disable error report parsing, as it fails with large reports

* Remove label definition because it's already specified in entity-base schema

* Remove ASCTB-TEMP prefix to enforce full IRI format for entity ID

* Set default label

* Use Date object to parse date string

* Fix file naming case collision in documentation

* Regenerating ER diagrams

* Add patch to define the ASCTB-TEMP prefix

* Update URIs for gene_expr and mean_gene_expr_value slots

* Enforce full URI usage for ASCTB-TEMP terms to prevent prefix-related issues

* Add support for DOI URLs containing dx.doi.org

* Set author ORCID field as optional in the schema

* Remove unused variable

* Add new slots

* Include the range for the create_date slot

* Set normalizeDate as a global function

* Patch the slot_id to use dcterms

* Fix passing parameter

* Return null when the RUI location is empty

* Collect the references from the array only

* Display the references in the README file, if available

* Change float range to decimal

* Remove references

* Update ER diagrams

* Breakdown long function

* Update OMAP schema to support reverse data reconstruction

* Bump version

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Co-authored-by: Josef Hardi <[email protected]>

Author: bherr2