BER Lakehouse Registry
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.
Download the registry as YAML: lakehouse-registry.yaml
To add or update an entry, edit lakehouse-registry.yaml in the repository root and open a pull request. Entries are validated against the registry schema in CI.
BRIDGE Lakehouse
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: other · Entries: 31
| Entry | Description | Owner (Contact) | Status | Access |
|---|---|---|---|---|
| nmdc-schema | National Microbiome Data Collaborative (NMDC) LinkML schema and submission schema. Field/element names are intended to be clearly defined with metadata, not ju… | Montana Smith | active | public |
| IDeA-schema | A schema for AI-driven enzyme discovery and biosynthetic pathway optimization. Represents a target reaction, the enzyme families ranked against it, candidate e… | Arvind Ramanathan | experimental | internal |
| plant phenotyping schema | Plant phenotyping schema for APPL (Advanced Plant Phenotyping Laboratory) based on the MIAPPE checklist and data model. | Priya Ranjan | experimental | public |
| lambda-ber-schema | A comprehensive LinkML schema for representing multimodal structural biology imaging data, from atomic-resolution structures to tissue-level organization. | Harry Caufield | active | public |
| aims-leaf | A schema for plant biology data, built on the lambda-ber-schema. | Sam Webb (Harry Caufield) | experimental | public |
| JBEI Ganymede | Plant protein expression and sample data from the JBEI Ganymede system. Only a pseudo-schema is available. | Chris Petzold (Valerie Skye) | experimental | internal |
| brc-schema | A schema for the Bioenergy Research Center portal. Describes properties of datasets in bioenergy, environmental science, earth science, and related fields. | Harry Caufield | active | public |
| osti-schema | 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… | Harry Caufield | active | public |
| kg-registry-schema | A schema defining properties and relationships between knowledge graphs, data resources, interfaces, tools, and documentation. Part of the KG-Registry project… | Harry Caufield | active | public |
| standards-schemas | A schema for metadata about biomedical data standards, including their AI/ML applications, related topics, substrates, organizations, and more. Part of the Bri… | Harry Caufield | active | public |
| data-sheets-schema | A schema for detailed metadata about biological and biomedical datasets. Implemented as part of the Bridge2AI project. | Marcin Joachimiak (Harry Caufield) | active | public |
| model-card-schema | A schema for detailed metadata about computational models. Implemented as part of the Bridge2AI project. | Marcin Joachimiak (Harry Caufield) | active | public |
| BERtron | Cross-BER sample metadata, geolocation-centric, with attributes, for NMDC, JGI, EMSL, ESS-DIVE. | Montana Smith (Sierra Moxon) | experimental | public |
| JGI GOLD | JGI project, sample, and analysis metadata (GOLD). | Valerie Skye | experimental | internal |
| JGI Study | Study metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. | Valerie Skye | experimental | internal |
| JGI Organism | Organism metadata from JGI GOLD, including plant and fungal isolates. Experimental LinkML projection for the Semantic Search service. | Valerie Skye | experimental | internal |
| JGI Biosample | Biosample metadata from JGI GOLD, including sample collection and ecosystem attributes. Experimental LinkML projection for the Semantic Search service. | Valerie Skye | experimental | internal |
| JGI Sequencing Project | Sequencing project metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. | Valerie Skye | experimental | internal |
| JGI Analysis Project | Analysis project metadata from JGI GOLD. Experimental LinkML projection for the Semantic Search service. | Valerie Skye | experimental | internal |
| kbase-cdm | KBase Central Data Model (CDM) schema. | AJ | active | public |
| kbase-credit | KBase Credit Metadata schema. | AJ | active | public |
| BASALT-Schema | MONet data model broadening to support EMSL in general. | Yuri Corilo | active | public |
| AmSC Open Metadata | 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 c… | Valerie Skye | experimental | restricted |
| CORAL | A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. In some ways more like a data modeling framework (like LinkM… | Unknown | active | public |
| GeoParquet | Parquet extension for geospatial data properties. | Unknown | active | public |
| linkml-test | A LinkML test schema. | Unknown | experimental | public |
| miappe-linkml | A LinkML representation of the MIAPPE plant phenotyping standard. Related to the plant phenotyping schema. | Unknown | experimental | public |
| pathogen-genomics-package | LinkML schema templates for pathogen genomics, including a wastewater template. | Unknown | experimental | public |
| nmdc-lakehouse-schema | A flattened LinkML representation of the NMDC schema for lakehouse use. Related to nmdc-schema. | Unknown | experimental | public |
| lakehouse-schema-extraction | Schemas extracted from lakehouse sources, represented in LinkML. | Unknown | experimental | public |
| ESS-DIVE Dataset Metadata | ESS-DIVE Dataset Metadata for publicly available datasets at ess-dive.lbl.gov. The Environmental System Science Data Infrastructure for a Virtual Ecosystem (ES… | ESS-DIVE (ESS-DIVE Support) | active | public |