Resources & Taxonomies

Table of contents

1. Introduction
2. Available Resources & Taxonomies
3. Submission Process
   1. Before Submitting
   2. Submitting New Entries
   3. Submission Guidelines
4. Tracking Submissions
   1. Monitoring Approval Status
   2. Responding to Feedback
5. After Approval
6. Next Steps

Introduction

BrainSTEM maintains standardized, controlled vocabularies for resources and taxonomies to ensure data consistency across the platform. As a user, you can contribute new entries when you encounter equipment, consumables, or taxonomic classifications that aren’t yet in the system. All submissions undergo an administrative review process to maintain data quality and prevent duplicates.

This tutorial guides you through submitting new resources and taxonomies, tracking their approval status, and using approved entries in your research documentation.

Available Resources & Taxonomies

Resources

Laboratory materials and equipment that can be submitted:

Resource Type	Description	Examples
Consumables	Materials used in experiments	Silicon probes, viral vectors, pharmaceutical agents, electrodes
Hardware devices	Electronic equipment and instruments	Recording systems, cameras, stimulation devices, microscopes
Suppliers	Vendors and manufacturers	Equipment manufacturers, chemical suppliers, research distributors

Taxonomies

Standardized classifications for biological and experimental categories:

Taxonomy Type	Description	Examples
Brain regions	Anatomical brain structures	Hippocampus CA1, Primary visual cortex, Basal ganglia
Setup types	Experimental environment categories	T-maze, Open field, Head-fixed disc, Surgical table
Species	Organism species	Mus musculus, Rattus norvegicus, Macaca mulatta
Strains	Genetic strains within species	C57BL/6J, Long-Evans, Sprague-Dawley

Submission Process

Before Submitting

Essential pre-submission checklist:

1. Search for existing entries: Check if the resource or taxonomy already exists to avoid duplicates
2. Gather complete information: Collect all necessary details:
   • For consumables: Product name, catalog number, supplier, specifications
   • For hardware devices: Manufacturer, model number, technical specifications, interface details
   • For taxonomies: Scientific names, standard references, descriptions
3. Verify accuracy: Double-check names, spellings, and technical specifications
4. Prepare documentation: Have links to manufacturer pages, datasheets, or scientific references ready

Submitting New Entries

To submit a new resource or taxonomy:

1. Navigate to the appropriate section:
   • Resources: Go to Resources → Select type (Consumables, Hardware devices, or Suppliers)
   • Taxonomies: Go to Taxonomies → Select type (Brain regions, Setup types, Species, or Strains)

2. Click the Add button for the resource or taxonomy type

3. Fill out the submission form with required information:

Resource/Taxonomy	Required Fields	Best Practices
Consumables	Product name, consumable type, supplier	Include catalog numbers, specifications, and intended use
Hardware devices	Manufacturer, model, device type	Provide technical specs, connectivity details, and compatible systems
Suppliers	Name, website, contact information	Include geographic regions served and product specialties
Setup types	Environment type name, category	Describe typical experimental use cases
Species	Scientific name, common name	Follow NCBI Taxonomy database conventions
Strains	Strain name, species, description	Include genetic background and supplier sources

1. Add detailed Description field content to help other users understand when to use this entry

2. Click Submit for admin review

Detailed descriptions speed up admin review and help other users select the correct entries. Include specifications, use cases, and any relevant technical details.

Submission Guidelines

Follow these standards for high-quality submissions:

• Use standard nomenclature: Follow established scientific naming conventions (e.g., NCBI for species)
• Be specific and descriptive:
  • Good: “NeuroNexus A1x32-Poly2 silicon probe, 32-channel, 25μm spacing”
  • Avoid: “Silicon probe”
• Include references: Cite manufacturer datasheets, or scientific classifications
• Check spelling carefully: Typos can cause rejection or create confusion in the database
• Avoid abbreviations without context: Define acronyms and technical terms in descriptions
• Provide manufacturer links: Include URLs to product pages or technical documentation where applicable

Tracking Submissions

Monitoring Approval Status

To check the status of your submissions:

1. Navigate to www.brainstem.org/private/approvals/
2. Review your submissions and their current status:

Status	Description	Action Required
Pending	Under administrative review	Wait for admin feedback; no action needed
Approved	Accepted and now available to all users	Entry is live; you can use it in your experiments
Rejected	Declined with feedback	Review comments and revise submission
Revision Requested	Needs modifications before approval	Address feedback and resubmit

1. Check the Comments field for detailed admin feedback or revision requests

Responding to Feedback

If your submission requires revisions:

1. Read admin comments carefully to understand specific concerns or needed improvements
2. Gather additional information if specifications, references, or details are requested
3. Make suggested changes to address each point of feedback
4. Resubmit following the same submission process
5. Add notes in the submission referencing the original entry and explaining your revisions

Common reasons for revision requests:

• Missing technical specifications or catalog numbers
• Unclear or ambiguous naming
• Duplicate entries (similar item already exists)
• Need for additional references or documentation
• Inconsistent formatting or nomenclature

Responding promptly to admin feedback speeds up the approval process. Most revisions are simple clarifications that can be addressed quickly.

After Approval

Once your submission is approved, it becomes part of the BrainSTEM platform:

Immediate effects:

• ✅ The entry appears in dropdown menus across BrainSTEM
• ✅ All users can select and reference the approved entry
• ✅ The entry becomes searchable in the resources/taxonomies database
• ✅ You can use it in your experimental documentation (setups, procedures, sessions)

Long-term impact:

• Your contribution helps standardize data across the research community
• Other labs can use your submissions, improving data interoperability
• The entry can be referenced in future resource submissions
• It becomes part of the permanent BrainSTEM vocabulary

Approved entries cannot be deleted but can be marked as deprecated if they become obsolete. Contact administrators if an entry needs updating.

Next Steps

After successfully contributing resources and taxonomies to BrainSTEM, consider these logical progressions:

• Set Up Your Lab Infrastructure: Use your newly approved resources in the Setting Up Lab Infrastructure tutorial to configure your own experimental setups with the equipment and suppliers you’ve contributed
• Begin Experimental Documentation: Start documenting your research using the Get Started tutorial and incorporate your approved resources into real experimental workflows
• Explore Specific Workflows: Depending on your research focus, dive into detailed experimental tutorials like Electrophysiology Workflow that will use your contributed resources
• Organize Your Team: Use Managing Projects and Managing Groups to organize access to your contributed resources across your research team
• Continue Contributing: As you discover new equipment, suppliers, or taxonomic categories in your research, continue expanding the BrainSTEM resource database by submitting additional entries