id: ber_registry:lakehouse-registry title: BER Lakehouse Registry description: >- The BER lakehouse registry. Schemas, standards, and reporting formats relevant to BER lakehouse data, imported from the BER data management "schema sources" tracking sheet. Each schema/standard is registered as a data source hosted (or planned to be hosted) in the BRIDGE lakehouse. This file is the registry itself: edit it to add or update entries, and validate with `just test`. lakehouses: - id: ber_registry:lakehouse-bridge-starburst title: BRIDGE Lakehouse description: >- Starburst-based BRIDGE data lakehouse serving as the primary hosting platform for data conforming to the registered BER schema sources. Platform is Starburst (Trino); recorded as 'other' because the PlatformType enum does not yet include starburst. operator: Lawrence Berkeley National Laboratory platform_type: other created_date: "2026-09-21" catalog_entries: - id: ber_registry:schema-nmdc-schema title: nmdc-schema description: >- National Microbiome Data Collaborative (NMDC) LinkML schema and submission schema. Field/element names are intended to be clearly defined with metadata, not just data labels. created_date: "2026-09-21" owner: Montana Smith contact_point: contact_name: Montana Smith contact_email: unknown@lbl.gov namespace: nmdc_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/microbiomedata/nmdc-schema facility: LBNL, PNNL project_affiliation: - NMDC keywords: - schema - linkml - microbiome format: - LinkML YAML data_quality_notes: >- Supports embargoed data and pipelines/workflows. See also the submission schema at https://github.com/microbiomedata/submission-schema. Collaborate with user groups/use cases to identify how to condense if need be. - id: ber_registry:schema-idea-schema title: IDeA-schema description: >- A schema for AI-driven enzyme discovery and biosynthetic pathway optimization. Represents a target reaction, the enzyme families ranked against it, candidate enzymes and their catalytic sites, predicted and mechanistically explained mutational effects on catalysis, and multi-enzyme pathways to a target molecule. Designed to run over federated DOE data (KBase, JGI, EMSL) accessed through the BER Data Lakehouse. created_date: "2026-09-21" owner: Arvind Ramanathan contact_point: contact_name: Arvind Ramanathan contact_email: unknown@lbl.gov namespace: idea_schema status: experimental is_deprecated: false update_schedule: unknown access_level: internal facility: ANL, ORNL project_affiliation: - Genesis Mission keywords: - schema - enzyme discovery - AI data_quality_notes: >- In development under the Genesis Mission / DOE BER IDeA (Intelligent Design Assistant) concept. Two-agent design: a discovery agent that ranks enzyme families against a plain reaction description, and a reasoner agent that predicts and explains mutational effects on catalysis. Class list is proposed and pending formal LinkML implementation; repo link and 'using LinkML' / 'production' status to be updated once the schema is stood up. Supports embargoed data and pipelines/workflows. - id: ber_registry:schema-plant-phenotyping title: plant phenotyping schema description: >- Plant phenotyping schema for APPL (Advanced Plant Phenotyping Laboratory) based on the MIAPPE checklist and data model. created_date: "2026-09-21" owner: Priya Ranjan contact_point: contact_name: Priya Ranjan contact_email: unknown@lbl.gov namespace: plant_phenotyping_schema status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/MIAPPE/MIAPPE/blob/master/MIAPPE_Checklist_Data_Model.pdf facility: ORNL project_affiliation: - APPL keywords: - schema - plant phenotyping - MIAPPE data_quality_notes: >- MIAPPE schema as a basis - needs a schema expert to work with Priya to go through it one by one. Valerie has started working with Swen Boehm to see how this corresponds to LAMBDA and AIMS-LEAF. Sam Webb and Harry were advised by Valerie in this project. Also see https://github.com/MIAPPE/MIAPPE/blob/master/MIAPPE_diagram.svg. - id: ber_registry:schema-lambda-ber-schema title: lambda-ber-schema description: >- A comprehensive LinkML schema for representing multimodal structural biology imaging data, from atomic-resolution structures to tissue-level organization. created_date: "2026-09-21" owner: Harry Caufield contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: lambda_ber_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/lambda-ber/lambda-ber-schema/tree/main/src/lambda_ber_schema/schema facility: LBNL, ANL, BNL, ORNL, PNNL, SLAC project_affiliation: - LAMBDA keywords: - schema - linkml - structural biology - imaging format: - LinkML YAML data_quality_notes: >- Supports embargoed data and pipelines/workflows. Beam/image/electron microscopy CryoEM data all resides close to instrumentation - various combinations of technical data, bespoke data management, overlapping vocabularies for annotating. - id: ber_registry:schema-aims-leaf title: aims-leaf description: >- A schema for plant biology data, built on the lambda-ber-schema. created_date: "2026-09-21" owner: Sam Webb contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: aims_leaf_schema status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/lambda-ber/aims-leaf/tree/main/src/aims_leaf_schema/schema facility: LBNL, SLAC project_affiliation: - AIMS-LEAF keywords: - schema - linkml - plant biology format: - LinkML YAML data_quality_notes: >- Sam Webb (SLAC) is responsible for this schema. Valerie Skye is also a DM team expert. AIMS-LEAF - beam. - id: ber_registry:schema-jbei-ganymede title: JBEI Ganymede description: >- Plant protein expression and sample data from the JBEI Ganymede system. Only a pseudo-schema is available. created_date: "2026-09-21" owner: Chris Petzold contact_point: contact_name: Valerie Skye contact_email: unknown@lbl.gov namespace: jbei_ganymede status: experimental is_deprecated: false update_schedule: unknown access_level: internal facility: LBNL project_affiliation: - OPAL - JBEI keywords: - schema - proteomics - plant biology data_quality_notes: >- Part of OPAL project. Chris Petzold is primary maintainer of the Ganymede lakehouse. Only a pseudo-schema is available. Sierra created ETL for Dremio: https://github.com/sierra-moxon/gbdq-ganymede. - id: ber_registry:schema-brc-schema title: brc-schema description: >- A schema for the Bioenergy Research Center portal. Describes properties of datasets in bioenergy, environmental science, earth science, and related fields. created_date: "2026-09-21" owner: Harry Caufield contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: brc_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/bioenergy-research-centers/brc-schema/tree/main/src/brc_schema/schema facility: LBNL, ORNL, Other project_affiliation: - BRC keywords: - schema - linkml - bioenergy format: - LinkML YAML data_quality_notes: >- Much (but not all) of the genome data is produced by JGI. Very publication-centric. Only public data is represented in the repo. See https://api.bioenergy.org/api/datasets and https://bioenergy.org/schema. Valerie Skye is also a DM team expert. - id: ber_registry:schema-osti-schema title: osti-schema description: >- A LinkML representation of the E-Link 2.0 schema used by OSTI. Includes slots for legacy compatibility with previous E-Link versions. Developed as part of the xBRC project. created_date: "2026-09-21" owner: Harry Caufield contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: osti_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/bioenergy-research-centers/brc-schema/blob/main/src/brc_schema/schema/osti_schema.yaml facility: LBNL, ORNL, Other project_affiliation: - xBRC keywords: - schema - linkml - OSTI - publications format: - LinkML YAML data_quality_notes: >- Published datasets, public focused, various kinds of datasets (genome, other), multiple versions of the schema in play at any time. Access raw data from each BRC, access combined data from Bioenergy.org. Candidate for lakehouse(s)? Chris Petzold is also PI here. Supports embargoed data and pipelines/workflows. - id: ber_registry:schema-kg-registry-schema title: kg-registry-schema description: >- A schema defining properties and relationships between knowledge graphs, data resources, interfaces, tools, and documentation. Part of the KG-Registry project (https://kghub.org/kg-registry/). created_date: "2026-09-21" owner: Harry Caufield contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: kg_registry_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/Knowledge-Graph-Hub/kg-registry/tree/main/src/kg_registry/kg_registry_schema/schema facility: LBNL project_affiliation: - KG-Registry keywords: - schema - linkml - knowledge graph format: - LinkML YAML data_quality_notes: >- Schema/graph to track KG projects that are already publicly available. Can we use this for our "lakehouse registry" schema? (PROV used here.) - id: ber_registry:schema-standards-schemas title: standards-schemas description: >- A schema for metadata about biomedical data standards, including their AI/ML applications, related topics, substrates, organizations, and more. Part of the Bridge2AI Standards Explorer (https://b2ai.standards.synapse.org/). created_date: "2026-09-21" owner: Harry Caufield contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: standards_schemas status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/bridge2ai/standards-schemas facility: LBNL, Other project_affiliation: - Bridge2AI keywords: - schema - linkml - data standards format: - LinkML YAML data_quality_notes: >- See also https://github.com/bridge2ai/b2ai-standards-registry/tree/main/src/schema (a mirror of the schema, used in production). - id: ber_registry:schema-data-sheets-schema title: data-sheets-schema description: >- A schema for detailed metadata about biological and biomedical datasets. Implemented as part of the Bridge2AI project. created_date: "2026-09-21" owner: Marcin Joachimiak contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: data_sheets_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/bridge2ai/data-sheets-schema facility: LBNL, Other project_affiliation: - Bridge2AI keywords: - schema - linkml - dataset metadata format: - LinkML YAML data_quality_notes: >- Marcin Joachimiak (LBNL) is responsible for this schema. In use on the Bridge2AI Standards Explorer. Supports embargoed data and pipelines/workflows. - id: ber_registry:schema-model-card-schema title: model-card-schema description: >- A schema for detailed metadata about computational models. Implemented as part of the Bridge2AI project. created_date: "2026-09-21" owner: Marcin Joachimiak contact_point: contact_name: Harry Caufield contact_email: unknown@lbl.gov namespace: model_card_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/bridge2ai/model-card-schema facility: LBNL, Other project_affiliation: - Bridge2AI keywords: - schema - linkml - model cards format: - LinkML YAML data_quality_notes: >- Marcin Joachimiak (LBNL) is responsible for this schema. Kjiersten was asking about this concept recently; Google has an Agentic Card quasi-standard: https://developers.googleblog.com/en/announcing-the-agentic-resource-discovery-specification/ - id: ber_registry:schema-bertron title: BERtron description: >- Cross-BER sample metadata, geolocation-centric, with attributes, for NMDC, JGI, EMSL, ESS-DIVE. created_date: "2026-09-21" owner: Montana Smith contact_point: contact_name: Sierra Moxon contact_email: smoxon@lbl.gov namespace: bertron status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://ber-data.github.io/bertron-schema/ facility: LBNL, PNNL project_affiliation: - BERtron keywords: - schema - linkml - sample metadata - geolocation format: - LinkML YAML data_quality_notes: >- NMDC, JGI, EMSL, ESS-DIVE combined catalog with sample, project, and other dataset metadata. Note: ESS-DIVE has alignment on dataset metadata (i.e., catalog info) but not ESS-DIVE sample metadata. Additional DM team experts: Montana Smith, Valerie Skye. - id: ber_registry:schema-jgi-gold title: JGI GOLD description: JGI project, sample, and analysis metadata (GOLD). created_date: '2026-09-21' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold status: experimental is_deprecated: false update_schedule: unknown access_level: internal facility: LBNL project_affiliation: - JGI keywords: - project metadata - sample metadata data_quality_notes: Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Entity-specific schemas are registered separately as jgi_gold_study, jgi_gold_organism, jgi_gold_biosample, jgi_gold_project, and jgi_gold_analysis. The API provides schema-shaped record projections separately from search results and embedding-oriented YAML. last_modified: '2026-10-14' documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads format: - LinkML YAML - YAML - JSON - id: ber_registry:schema-jgi-gold-study title: JGI Study description: Study metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. created_date: '2026-09-30' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold_study status: experimental is_deprecated: false update_schedule: irregular access_level: internal documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads facility: JGI project_affiliation: - JGI - GOLD keywords: - schema - linkml - GOLD - study metadata format: - LinkML YAML version: 0.1.0 lineage: Derived from JGI GOLD and its Semantic Data Dictionary, with reviewed NMDC mappings and GOLD extensions. data_quality_notes: 'Schema source: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/schemas/gold_study.yaml?ref_type=heads Schema identifier: https://w3id.org/bridge/gold/study. Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Relative API paths (no production base URL assigned): GET /api/linkml/entities/study for the generated schema; GET /api/linkml/entities/study/{identifier}/record for a schema-shaped record. YAML is the default response; ?format=json requests JSON. Repository schema snapshots and live dictionary-generated schemas may evolve separately.' - id: ber_registry:schema-jgi-gold-organism title: JGI Organism description: Organism metadata from JGI GOLD, including plant and fungal isolates. Experimental LinkML projection for the Semantic Search service. created_date: '2026-09-30' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold_organism status: experimental is_deprecated: false update_schedule: irregular access_level: internal documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads facility: JGI project_affiliation: - JGI - GOLD keywords: - schema - linkml - GOLD - organism metadata format: - LinkML YAML version: 0.1.0 lineage: Derived from JGI GOLD and its Semantic Data Dictionary, with reviewed NMDC mappings and GOLD extensions. data_quality_notes: 'Schema source: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/schemas/gold_organism.yaml?ref_type=heads Schema identifier: https://w3id.org/bridge/gold/organism. Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Relative API paths (no production base URL assigned): GET /api/linkml/entities/organism for the generated schema; GET /api/linkml/entities/organism/{identifier}/record for a schema-shaped record. YAML is the default response; ?format=json requests JSON. Repository schema snapshots and live dictionary-generated schemas may evolve separately.' - id: ber_registry:schema-jgi-gold-biosample title: JGI Biosample description: Biosample metadata from JGI GOLD, including sample collection and ecosystem attributes. Experimental LinkML projection for the Semantic Search service. created_date: '2026-09-30' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold_biosample status: experimental is_deprecated: false update_schedule: irregular access_level: internal documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads facility: JGI project_affiliation: - JGI - GOLD keywords: - schema - linkml - GOLD - biosample metadata format: - LinkML YAML version: 0.1.0 lineage: Derived from JGI GOLD and its Semantic Data Dictionary, with reviewed NMDC mappings and GOLD extensions. data_quality_notes: 'Schema source: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/schemas/gold_biosample.yaml?ref_type=heads Schema identifier: https://w3id.org/bridge/gold/biosample. Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Relative API paths (no production base URL assigned): GET /api/linkml/entities/biosample for the generated schema; GET /api/linkml/entities/biosample/{identifier}/record for a schema-shaped record. YAML is the default response; ?format=json requests JSON. Repository schema snapshots and live dictionary-generated schemas may evolve separately.' - id: ber_registry:schema-jgi-gold-project title: JGI Sequencing Project description: Sequencing project metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. created_date: '2026-09-30' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold_project status: experimental is_deprecated: false update_schedule: irregular access_level: internal documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads facility: JGI project_affiliation: - JGI - GOLD keywords: - schema - linkml - GOLD - project metadata format: - LinkML YAML version: 0.1.0 lineage: Derived from JGI GOLD and its Semantic Data Dictionary, with reviewed NMDC mappings and GOLD extensions. data_quality_notes: 'Schema source: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/schemas/gold_project.yaml?ref_type=heads Schema identifier: https://w3id.org/bridge/gold/project. Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Relative API paths (no production base URL assigned): GET /api/linkml/entities/project for the generated schema; GET /api/linkml/entities/project/{identifier}/record for a schema-shaped record. YAML is the default response; ?format=json requests JSON. Repository schema snapshots and live dictionary-generated schemas may evolve separately.' - id: ber_registry:schema-jgi-gold-analysis title: JGI Analysis Project description: Analysis project metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. created_date: '2026-09-30' owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: vaskye@lbl.gov namespace: jgi_gold_analysis status: experimental is_deprecated: false update_schedule: irregular access_level: internal documentation_url: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/README.md?ref_type=heads facility: JGI project_affiliation: - JGI - GOLD keywords: - schema - linkml - GOLD - analysis metadata format: - LinkML YAML version: 0.1.0 lineage: Derived from JGI GOLD and its Semantic Data Dictionary, with reviewed NMDC mappings and GOLD extensions. data_quality_notes: 'Schema source: https://code.jgi.doe.gov/dsi/advanced-analysis/data-modeling/semantic-search/-/blob/main/schemas/gold_analysis.yaml?ref_type=heads Schema identifier: https://w3id.org/bridge/gold/analysis. Schemas are experimental and intended to become public; repository URLs are currently internal. The Semantic Search service runs locally and is not yet deployed on a production server. Schemas are updated intermittently, while source records are updated daily. Schemas are based in part on NMDC and are expected to evolve toward alignment with bridge-central-schema once available. Relative API paths (no production base URL assigned): GET /api/linkml/entities/analysis for the generated schema; GET /api/linkml/entities/analysis/{identifier}/record for a schema-shaped record. YAML is the default response; ?format=json requests JSON. Repository schema snapshots and live dictionary-generated schemas may evolve separately.' - id: ber_registry:schema-kbase-cdm title: kbase-cdm description: KBase Central Data Model (CDM) schema. created_date: "2026-09-21" owner: AJ contact_point: contact_name: AJ contact_email: unknown@lbl.gov namespace: kbase_cdm status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://kbase.github.io/cdm-schema/ facility: LBNL project_affiliation: - KBase keywords: - schema - linkml - central data model format: - LinkML YAML data_quality_notes: KBase CDM and Credit Metadata schema. - id: ber_registry:schema-kbase-credit title: kbase-credit description: KBase Credit Metadata schema. created_date: "2026-09-21" owner: AJ contact_point: contact_name: AJ contact_email: unknown@lbl.gov namespace: kbase_credit status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://www.kbase.us/news/kbase-credit-metadata-schema/ facility: LBNL project_affiliation: - KBase keywords: - schema - linkml - credit metadata format: - LinkML YAML - id: ber_registry:schema-basalt-schema title: BASALT-Schema description: >- MONet data model broadening to support EMSL in general. created_date: "2026-09-21" owner: Yuri Corilo contact_point: contact_name: Yuri Corilo contact_email: unknown@lbl.gov namespace: basalt_schema status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/EMSL-Computing/BASALT-Schema facility: PNNL project_affiliation: - MONet - EMSL keywords: - schema - linkml - soil format: - LinkML YAML data_quality_notes: >- Currently managed on the PNNL internal GitLab but included here because Montana, Yuri, and Bea all work on it and similar modelling is being built out. - id: ber_registry:schema-amsc-open-metadata title: AmSC Open Metadata description: >- American Science Cloud (AmSC) Open Metadata. Not for data loading into the lakehouse, but something the registry may need to conform or map to in order to be compatible with Open Metadata / American Science Cloud. They are working on permission support / access control. created_date: "2026-09-21" owner: Valerie Skye contact_point: contact_name: Valerie Skye contact_email: unknown@lbl.gov namespace: amsc_open_metadata status: experimental is_deprecated: false update_schedule: unknown access_level: restricted facility: Other keywords: - metadata standard - access control data_quality_notes: >- Not publicly available. Valerie Skye and Val Hendrix have access. Karlo Berket is also a good contact for this. Supports embargoed data. - id: ber_registry:schema-coral title: CORAL description: >- A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. In some ways more like a data modeling framework (like LinkML), but with support for defining specific data types in terms of their parameters, properties, etc. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: coral status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/jmchandonia/CORAL facility: LBNL project_affiliation: - ENIGMA keywords: - data modeling framework data_quality_notes: Applied in the ENIGMA project. - id: ber_registry:schema-geoparquet title: GeoParquet description: Parquet extension for geospatial data properties. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: geoparquet status: active is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://geoparquet.org/releases/v1.1.0/ facility: Other keywords: - reference standard - geospatial - parquet - id: ber_registry:schema-linkml-test title: linkml-test description: A LinkML test schema. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: linkml_test status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/pranjan77/linkml-test/blob/main/src/linkml_test/schema/linkml_test.yaml keywords: - schema - linkml format: - LinkML YAML - id: ber_registry:schema-miappe-linkml title: miappe-linkml description: >- A LinkML representation of the MIAPPE plant phenotyping standard. Related to the plant phenotyping schema. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: miappe_linkml status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/sierra-moxon/miappe-linkml/blob/main/src/miappe_linkml/schema/miappe_linkml.yaml keywords: - schema - linkml - plant phenotyping - MIAPPE format: - LinkML YAML - id: ber_registry:schema-pathogen-genomics-package title: pathogen-genomics-package description: >- LinkML schema templates for pathogen genomics, including a wastewater template. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: pathogen_genomics_package status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/cidgoh/pathogen-genomics-package/blob/main/templates/wastewater/schema.yaml keywords: - schema - linkml - pathogen genomics format: - LinkML YAML - id: ber_registry:schema-nmdc-lakehouse-schema title: nmdc-lakehouse-schema description: >- A flattened LinkML representation of the NMDC schema for lakehouse use. Related to nmdc-schema. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: nmdc_lakehouse_schema status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/microbiomedata/nmdc-lakehouse-schema/blob/main/src/nmdc_lakehouse_schema/schema/nmdc_schema_flattened.yaml project_affiliation: - NMDC keywords: - schema - linkml - microbiome format: - LinkML YAML - id: ber_registry:schema-lakehouse-schema-extraction title: lakehouse-schema-extraction description: >- Schemas extracted from lakehouse sources, represented in LinkML. created_date: "2026-09-21" owner: Unknown contact_point: contact_name: Unknown contact_email: unknown@lbl.gov namespace: lakehouse_schema_extraction status: experimental is_deprecated: false update_schedule: unknown access_level: public documentation_url: https://github.com/sierra-moxon/lakehouse-schema-extraction/tree/main/schemas keywords: - schema - linkml - schema extraction format: - LinkML YAML data_quality_notes: >- Needs checking subdirectories for LinkML YAML. - id: ber_registry:essdive-dataset-metadata title: ESS-DIVE Dataset Metadata description: >- ESS-DIVE Dataset Metadata for publicly available datasets at ess-dive.lbl.gov. The Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) is a data repository for Earth and environmental sciences. ESS-DIVE stores data generated from research funded by or related to the DOE’s Office of Science Biological and Environmental Research program (BER). This includes a variety of observational, experimental, modeling and other data products from a wide range of ecological and urban systems. The Dataset Metadata fully describe datasets to FAIR standards so that others can more easily find and use relevant data from dataset searches. created_date: "2026-09-29" last_modified: "2026-09-29" owner: ESS-DIVE contact_point: contact_name: ESS-DIVE Support contact_email: ess-dive-support@lbl.gov namespace: essdive_dataset_metadata status: active is_deprecated: false update_schedule: unknown access_level: public keywords: - dataset metadata - environmental science project_affiliation: - ESS-DIVE license: CC0 facility: LBNL documentation_url: https://github.com/ess-dive/essdive-linkml-schemas modality: metadata data_quality_notes: >- ESS-DIVE Dataset Metadata records are reviewed by ESS-DIVE staff for completeness and compliance with FAIR standards.