Updating "Getting Started" information #61
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| <template> | ||
| <q-page class="column items-center"> | ||
| <PageTitle title="Standards" subtitle="EMBER interoperability & reproducibility" /> | ||
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| <div class="q-mx-xl full-width max-w-screen-lg"> | ||
| <q-card flat class="q-mt-lg"> | ||
| <q-card-section> | ||
| <div class="text-h4 q-mb-md">Overview</div> | ||
| <p> | ||
| EMBER adopts community standards to enable interoperability and reproducibility across multimodal neuroscience datasets. | ||
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| This page outlines the data and metadata standards integrated by EMBER, workflow guidance for users, validation tools, | ||
| and EMBER-specific conventions. | ||
| </p> | ||
| </q-card-section> | ||
| </q-card> | ||
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| <q-expansion-item label="Data Standards (NWB, BIDS)" icon="schema" class="q-mt-md"> | ||
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| <div class="q-pa-md"> | ||
| <p>EMBER integrates widely used community standards for data organization:</p> | ||
| <ul> | ||
| <li><strong>NWB:</strong> for neurophysiology (ephys, behavior, optophysiology)</li> | ||
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| <li><strong>BIDS:</strong> for MRI, EEG/MEG/iEEG, microscopy, derivatives</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Metadata Standards" icon="list_alt" class="q-mt-sm"> | ||
| <div class="q-pa-md"> | ||
| <p>EMBER enforces core metadata fields and encourages controlled vocabularies/ontologies:</p> | ||
| <ul> | ||
| <li>Required fields: project, subject/session IDs, modality, acquisition date</li> | ||
| <li>Controlled vocabularies: species, anatomy, device names</li> | ||
| <li>Ontologies: Uberon (anatomy), NCBI Taxonomy, behavior/task ontologies</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Workflow Guidance" icon="directions" class="q-mt-sm"> | ||
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| <div class="q-pa-md"> | ||
| <ol> | ||
| <li>Organize/convert data into NWB or BIDS formats</li> | ||
| <li>Populate metadata fields (use controlled vocabularies where possible)</li> | ||
| <li>Run local validators and fix errors/warnings</li> | ||
| <li>Prepare ancillary files (README, code, notes)</li> | ||
| <li>Upload via EMBER‑DANDI</li> | ||
| </ol> | ||
| <p class="text-caption">Restricted workflows will be added once finalized.</p> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Validation Tools & Services" icon="verified" class="q-mt-sm"> | ||
| <div class="q-pa-md"> | ||
| <ul> | ||
| <li>NWB Validator: checks file structure and metadata</li> | ||
| <li>BIDS Validator: checks directory layout, filenames, sidecars</li> | ||
| <li>EMBER‑DANDI server‑side checks during upload</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="EMBER‑Specific Conventions" icon="description" class="q-mt-sm q-mb-xl"> | ||
| <div class="q-pa-md"> | ||
| <ul> | ||
| <li>Naming rules: dataset IDs, subject/session formats (lowercase + underscores)</li> | ||
| <li>Schema snippets: JSON/YAML examples for common metadata blocks</li> | ||
| <li>Templates: starter JSON sidecars and field checklists</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
| </div> | ||
| </q-page> | ||
| </template> | ||
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| <script setup lang="ts"> | ||
| import PageTitle from 'src/components/PageTitle.vue'; | ||
| </script> | ||
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| @@ -0,0 +1,77 @@ | ||
| <template> | ||
| <q-page class="column items-center"> | ||
| <PageTitle title="Workflow Guidance" subtitle="Steps for ingest, validation, and data submission" /> | ||
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| <div class="q-mx-xl full-width max-w-screen-lg"> | ||
| <q-card flat class="q-mt-lg"> | ||
| <q-card-section> | ||
| <div class="text-h4 q-mb-md">Overview</div> | ||
| <p> | ||
| This page provides detailed workflow guidance for preparing, validating, and submitting data to the EMBER ecosystem. | ||
| It is intended to help users follow a consistent process to ensure interoperability, reproducibility, and compliance | ||
| with community standards. | ||
| </p> | ||
| </q-card-section> | ||
| </q-card> | ||
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| <q-expansion-item label="Step 1: Organize Data" icon="folder" class="q-mt-md"> | ||
| <div class="q-pa-md"> | ||
| <p>Convert or organize raw data into recognized community formats where possible:</p> | ||
| <ul> | ||
| <li>Use NWB for neurophysiology and behavioral time series</li> | ||
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| <li>Use BIDS for imaging, EEG/MEG/iEEG, and derivatives</li> | ||
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| <li>Maintain consistent folder structures and naming conventions</li> | ||
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| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Step 2: Populate Metadata" icon="list_alt" class="q-mt-sm"> | ||
| <div class="q-pa-md"> | ||
| <p>Fill in required metadata fields and, where possible, use controlled vocabularies and ontologies:</p> | ||
| <ul> | ||
| <li>Project, dataset, subject, and session identifiers</li> | ||
| <li>Species, anatomy, device, and modality information</li> | ||
| <li>Acquisition dates, license, and contributors</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Step 3: Validate Data" icon="verified" class="q-mt-sm"> | ||
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| <div class="q-pa-md"> | ||
| <p>Run validation tools to confirm compliance:</p> | ||
| <ul> | ||
| <li><strong>NWB Validator</strong>: checks internal structure and metadata completeness</li> | ||
| <li><strong>BIDS Validator</strong>: checks directory layout, filenames, and sidecars</li> | ||
| <li><strong>EMBER-DANDI Checks</strong>: automated validation during upload</li> | ||
| </ul> | ||
| <p class="text-caption">Address any validation errors or warnings before submission.</p> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Step 4: Prepare Ancillary Files" icon="description" class="q-mt-sm"> | ||
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| <div class="q-pa-md"> | ||
| <ul> | ||
| <li>README files describing dataset contents and organization</li> | ||
| <li>Methodological notes or data processing scripts</li> | ||
| <li>Supplementary documentation (e.g., experimental protocols)</li> | ||
| </ul> | ||
| </div> | ||
| </q-expansion-item> | ||
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| <q-expansion-item label="Step 5: Submit to EMBER" icon="cloud_upload" class="q-mt-sm q-mb-xl"> | ||
| <div class="q-pa-md"> | ||
| <ol> | ||
| <li>Ensure you have registered for EMBER-DANDI with your GitHub account</li> | ||
| <li>Use the DANDI CLI or UI to upload validated datasets</li> | ||
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| <li>Retain validation logs and ancillary files with the dataset</li> | ||
| </ol> | ||
| <p class="text-caption">Restricted workflows (e.g., sensitive or controlled-access data) will be added once finalized.</p> | ||
| </div> | ||
| </q-expansion-item> | ||
| </div> | ||
| </q-page> | ||
| </template> | ||
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| <script setup lang="ts"> | ||
| import PageTitle from 'src/components/PageTitle.vue'; | ||
| </script> | ||
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Is "Data Ingest Guidnace" or "Data Upload Guidance" more accessible to users? I wonder if that will be easier for the non-expert user to quickly understand.
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+1 to adding extra words to describe which type of workflow this documentation is about (sometimes people have a lot of 'workflows' floating around for all kinds of things)