Refactor add cds imaging

[Bankso]

Fixes #116

Once merging, we should wait to create a release until 1) models have been reviewed internally and 2) data model explorer documentation has been updated

Changelog

This PR integrates several new metadata attributes, valid values, and models. Most attributes and valid values were adapted from those used in CDS/CRDC and HTAN models. The attributes were renamed, if necessary for clarity, and assembled into a set of models intended to capture file information and experimental details. CDS/CRDC source materials are available here:

• CDS Imaging V1.0 (released June 2024)
• CDS Metadata Submission Template V1.3.3

Note: Attribute mappings in these sheets are being converted to a formal reference document that will be integrated into the data-models repository

Guidance on working with the updated data model is in preparation here, alongside info on all other resource management infrastructure elements.

The model expansion and redesign also includes an updated information linking framework, which employs primary ("component_id") and foreign keys ("component Key") to define connections between records and/or files. Information on the _id/Key system is contained in Appendices of the guidance doc linked above.

Updated templates are available in the repo as CSVs. Google sheet links for review:

Record manifests

• Biospecimen: https://docs.google.com/spreadsheets/d/1u6OhS-8JNZ66tHY3qCGfecB8MNYzNzhy_IELJybGoWA
• Dataset Sharing Plan: https://docs.google.com/spreadsheets/d/1XPzHiUPtxO2m3nBzYTvvUZ_nbiZq-Gieef3OFiHPwoA
• Dataset View: https://docs.google.com/spreadsheets/d/1sbrfCk4w2J-s6JOKoHzXwvFwUUw3cP31lWL1JRwTCp8
• Educational Resources: https://docs.google.com/spreadsheets/d/1vYDtwDvyrfzFJ7PrcHHiV0EPHaf2xRF1OQrmfYJTSos
• Grant View: https://docs.google.com/spreadsheets/d/1TB3MC5dv9QxKB-twvB-tE69fAkJHGtuzCC8Ucavwqvc
• Individual: https://docs.google.com/spreadsheets/d/1IZtQc-5lcQu-juWHjp14PeicoLjYGGh8aJnqZ8fWWEk
• Study: https://docs.google.com/spreadsheets/d/1taLSRvGel0DSwkl8i7INEO9U9wKf7RVFBJwT_3TIYlY
• Model: https://docs.google.com/spreadsheets/d/13P9GlXyKsxr4vUR7e-2ZnIuiTKw0JwaSP5jHjiKYoFI
• Person View: https://docs.google.com/spreadsheets/d/1M59Qw3psOJjThOzgVWOKXH-vSlwt65yHW3VgNqF81fU
• Publication View: https://docs.google.com/spreadsheets/d/10Kmb3m_p8UMtHNjuz7AtHdgRAEbwA-X_8LiCfgIXeIc
• Project View: https://docs.google.com/spreadsheets/d/1dlOUr2Jf34miQ5-ZsyXITJ3PyCtLcaqRb41ONhA3VyM
• Tool View: https://docs.google.com/spreadsheets/d/1W4zDrf_iMX47s4rJexkosZZ0_zbqjSOtxd215D64p4c

File manifests

• File View: https://docs.google.com/spreadsheets/d/16JgWUOJYK_eOlVcxNVAks4uuECF-8e63zu9IGBkATOM

Imaging manifests

• Imaging Channel: https://docs.google.com/spreadsheets/d/1RnN47Wbfe9tXWLtG3t8OYYFUEc9PiHELpSkwCUh1ORs
• Imaging Level 1: https://docs.google.com/spreadsheets/d/1e5O6LaaRQX8XCNahzqx_u1jiI3ZN-0zHjUkaWAIRqCM
• Imaging Level 2: https://docs.google.com/spreadsheets/d/19nhFD_NXK7vzn2oMK9lj26fgokayfCSaNl7rFII31to
• Imaging Level 3 Image: https://docs.google.com/spreadsheets/d/19k-3KbUJl8RfB49sGmiVCA7HmF4AhXiZXBTVr5xzGsA
• Imaging Level 3 Segments: https://docs.google.com/spreadsheets/d/1vDuN0FEnG0IBv69sXfgyJjP4x9maa3onp3tHl4PVxXQ
• Imaging Level 4: https://docs.google.com/spreadsheets/d/1xvV5YpOk-fHa4PtgTzIokht-340_p0SjOMTqnAXBaRQ

Nanostring GeoMx manifests

• Nanostring GeoMx DSP Auxiliary Files: https://docs.google.com/spreadsheets/d/1zfcXb-tdCrbrPgdZreVUZ7YwVbx-bEhnPy31GySAcBc
• Nanostring GeoMx DSP Level 1: https://docs.google.com/spreadsheets/d/18sVPMQiUbieXwQFPvU83_y16p5jIfiwVaTEiOKcYmtA
• Nanostring GeoMx DSP Level 2: https://docs.google.com/spreadsheets/d/1cWEaInw2X35jPgX7Y-CYPoP6qGJ_FZDX4mXoiy50ziA
• Nanostring GeoMx DSP Level 3: https://docs.google.com/spreadsheets/d/12ncJmBej2hQcOIJEJRTzwDwEYWWF2IZnEi7jHGlXRXM
• Nanostring GeoMx ROI Segment Annotations: https://docs.google.com/spreadsheets/d/11gP89QoM0J7_lndmvM9bmjORFCbZ4nSj99tWdbofmZQ
• Nanostring GeoMx Imaging: https://docs.google.com/spreadsheets/d/1sFWPIXAsOQABcQz7w5V0gAzd5UEIQ-0Rw0H2Pvo2YEE

Sequencing manifests

• Sequencing Level 1: https://docs.google.com/spreadsheets/d/1_0kJUWd0xB9SOPHupsIxNi80JVtrcpmD9pSAUtNtUho
• Sequencing Level 2: https://docs.google.com/spreadsheets/d/1LSvW8XmdYUhAkW41mWHuXP-yBd3FjXBbAIcYb8mjloA
• Sequencing Level 3: https://docs.google.com/spreadsheets/d/16e6ZCIPCo5qKBrK3W65QDNQ5s9KAvW1vN_-W1IAY72c

10x Visium manifests

• 10x Visium Auxiliary Files: https://docs.google.com/spreadsheets/d/1Dt_UBvTN3oQJ02V3uHM6jLyRpocZs0a7zbmDRi_iDeE
• 10x Visium RNA Level 1: https://docs.google.com/spreadsheets/d/1v8Aq2uktFdRee8S2wKa-ue4j9udwzqtoMFy1a5X6VRo
• 10x Visium RNA Level 2: https://docs.google.com/spreadsheets/d/1uxNESaIBHXPGYCWUx6GvzWSTtGtFPhHYHASaYxl01tM
• 10x Visium RNA Level 3: https://docs.google.com/spreadsheets/d/11AhVmLuUMbyiOnls_ibwjM39O_sWCc_AWeAg9RSNYtU
• 10x Visium RNA Level 4: https://docs.google.com/spreadsheets/d/1rQiFltAWfEiJYFMLrfilduG5feBla9IqpT5f_xpskDk