slug: benchling provider: Benchling generated_by: planning/capability-mapping/scripts/classify_capabilities.py model: claude-opus-5 frame: - Pharmaceuticals & Life Sciences min_confidence: 0.7 capability_model: source: https://github.com/vincentmakes/turbo-ea-capabilities license: CC-BY-4.0 attribution: Turbo EA Capabilities by Vincent Verdet — Turbo EA, https://github.com/vincentmakes/turbo-ea-capabilities, CC BY 4.0 notice: NOTICE edge_count: 32 edges: - tag: SqlDashboard spec_file: benchling-sqldashboard-api-openapi.yml capability_id: BC-610.50 capability_id_l1: BC-610 capability_name: Analytics & BI Management confidence: 0.85 evidence: '"a configurable analytics page that displays one or more SQL-driven visualizations within Benchling Insights" ... "SQL Dashboards query Benchling''s data warehouse"' reason: Dashboards of SQL-driven charts/tables over a data warehouse are business intelligence and analytics delivery. - tag: SqlDashboardBlock spec_file: benchling-sqldashboardblock-api-openapi.yml capability_id: BC-610.50 capability_id_l1: BC-610 capability_name: Analytics & BI Management confidence: 0.85 evidence: '"Each block contains a SQL query (sqlQuery) that runs against the Benchling data warehouse, along with a BlockVisualization"' reason: Query-and-visualisation panes for analytics dashboards realise Analytics & BI Management. - tag: Policy spec_file: benchling-policy-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.8 evidence: '"Defines a named set of permissions that can be assigned to users or groups through collaborations. Policies contain PolicyStatements that specify allowed actions"; "Common policies include viewer (read-only access), editor ... admin"' reason: 'Despite ''Policy'' being a homograph for corporate policy management, here it is an authorisation construct: named permission sets with statements granting actions to users and groups. That is squarely identity and access management, not BC-130.20 policy lifecycle.' - tag: ProcedureRun spec_file: benchling-procedurerun-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.78 evidence: '"An active execution of a procedure template. Created when scientists start running an experiment based on a `Procedure` ... Also known as an "experiment" in the Benchling UI."' reason: Directly represents execution of a laboratory experiment with conditions and replicates — squarely lab experimentation within R&D management. - tag: Assay Runs spec_file: benchling-assay-runs-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.75 evidence: GET /assay-runs listAssayRuns 'List runs'; schemas 'AssayRun', 'AutomationInputGenerator', 'LabAutomationTransform' reason: Operations create, read and archive laboratory assay runs with lab-automation input/output files — i.e. execution and tracking of experiments. Best fits R&D experimentation/lab work rather than any SaaS-product or cross-industry business capability. Not a technical-plumbing tag. recovered_from: sweep-20260828T235257Z-edges.json - tag: Collaboration spec_file: benchling-collaboration-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.75 evidence: '"A Collaboration indicates that a Principal or Group is granted a Policy on a Resource. Some Collaborations represent Ownership, while others indicate that a Resource was shared with the Principal or Group."' reason: Despite the collaborative-sounding name, the operations grant and revoke policies for principals, groups, teams and organizations over resources — access-permission administration. Schemas PolicyRef, PrincipalRef, GroupCollaboratorInfo confirm authorisation, not scientific collaboration. - tag: Molecule spec_file: benchling-molecule-api-openapi.yml capability_id: BC-1500.60 capability_id_l1: BC-1500 capability_name: Compound & Library Management confidence: 0.75 evidence: '"A Molecule represents a small molecule chemical compound in Benchling ... Molecules are registry entities that can be registered, searched, and linked to other items"' reason: CRUD and bulk registration of small-molecule chemical compounds in a registry with canonical SMILES — this is compound/library repository management within drug discovery R&D. - tag: Molecules spec_file: benchling-molecules-api-openapi.yml capability_id: BC-1500.60 capability_id_l1: BC-1500 capability_name: Compound & Library Management confidence: 0.75 evidence: '"PATCH /molecules/{entity_registry_id}:upsert upsertMolecule Create or update a registered Molecule"' reason: Registration and bulk upsert of chemical compound entities into the research registry — compound and library/repository management in discovery. Title mentioning AA Sequences is spec-splitting noise; operations are all molecules. - tag: Organization spec_file: benchling-organization-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.75 evidence: '"Users are designated as either ADMIN (with management privileges) or MEMBER within the organization via `GroupMembership`"; "Organizations also control access settings"; operation "List GroupMembership items"' reason: 'Despite the business-sounding noun, this tag is a user-group and access-control construct: group membership, admin/member roles, and default access policies. That is identity and access management, not any corporate-entity or organisational-design capability.' - tag: Organizations spec_file: benchling-organizations-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.75 evidence: '"POST /organizations/{organization_id}/memberships createOrganizationMembership"; "DELETE /organizations/{organization_id}/memberships/{user_id}"; schemas "Membership", "UserSummary"' reason: Operations administer user membership in access-control groups (create, update, delete membership by user id). This is joiner/mover/leaver style identity and access administration within the platform, not corporate entity management. - tag: ProcedureRunConditionReplicate spec_file: benchling-procedurerunconditionreplicate-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.75 evidence: '"Scientists often run the same experimental condition multiple times to obtain statistically significant results—each repetition is a replicate"' reason: Replicate management for experimental runs is core lab experimentation practice. - tag: ProcedureRunPlan spec_file: benchling-procedurerunplan-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.75 evidence: '"A draft experiment plan that can be promoted to a `ProcedureRun` for execution. Scientists use run plans to configure experimental conditions, parameter values, and replicates before starting an actual experiment."' reason: Planning and promotion of laboratory experiments — experimentation management within R&D. Not project/portfolio management despite the 'plan' noun. - tag: Study spec_file: benchling-study-api-openapi.yml capability_id: BC-810.10 capability_id_l1: BC-810 capability_name: Research Management confidence: 0.75 evidence: '"A structured unit used to plan and organize research in Benchling. Each study progresses through phases ... from design to execution to completion"; "Create Study", "Update Study"' reason: Operations create and manage research studies through design-to-completion phases, which is directly research management within R&D. recovered_from: sweep-20260828T235257Z-edges.json - tag: Location spec_file: benchling-location-api-openapi.yml capability_id: BC-530 capability_id_l1: BC-530 capability_name: Inventory Management confidence: 0.72 evidence: '"A Location represents a physical storage area in Benchling''s inventory system, such as a freezer, refrigerator, shelf, room, or building" ... "Each location tracks its capacity (totalCapacity, availableCapacity, occupiedCapacity)"' reason: Operations create/list/update physical storage locations with capacity tracking and barcode identification within an inventory system — this realises inventory/stock location management. No sub-capability cleanly covers storage-location hierarchy, so only L1 is asserted. recovered_from: sweep-20260828T235257Z-edges.json - tag: ProcedureMethodExecutionInstance spec_file: benchling-proceduremethodexecutioninstance-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.72 evidence: '"When a scientist runs a procedure, each method in the flowchart becomes a ProcedureMethodExecutionInstance that tracks the actual execution: the worksheet where data is entered"' reason: Tracks actual laboratory execution of experimental methods and captured parameter values — lab work / experimentation execution within R&D. recovered_from: sweep-20260828T235257Z-edges.json - tag: ProcedureParameterMeasuredValue spec_file: benchling-procedureparametermeasuredvalue-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.72 evidence: '"Records the actual measured or observed value for a parameter during procedure execution. Scientists enter measured values after performing an experimental step—for example, recording a temperature reading, an absorbance measurement"' reason: 'Capture of experimental measurement data during lab procedure execution on an R&D lab platform — this is laboratory experimentation, best matched to Experimentation & Prototyping Management (lab work). Not clinical or GxP QC: the context describes generic bench science, so confidence is moderate.' - tag: ProcedureRunCondition spec_file: benchling-procedureruncondition-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.72 evidence: '"a configuration of the methods of a Procedure that is being executed within a ProcedureRun"' reason: Experimental condition configuration within an executing experiment — part of laboratory experimentation, not a commercial or manufacturing process. - tag: ProcedureRunPlanCondition spec_file: benchling-procedurerunplancondition-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.72 evidence: '"Scientists use conditions to plan different experimental configurations before execution—for example, testing multiple temperatures or reagent concentrations"' reason: Pre-execution design of experimental conditions — lab experimentation planning. - tag: Boxes spec_file: benchling-boxes-api-openapi.yml capability_id: BC-1500.60 capability_id_l1: BC-1500 capability_name: Compound & Library Management confidence: 0.7 evidence: '"GET /boxes/{box_id}/contents listBoxContents List a box''s contents"; "POST /boxes:archive archiveBoxes"' reason: Operations create, update, archive and enumerate contents of physical storage boxes in the lab inventory — sample repository/library management in a life-sciences R&D context. The OpenAPI title/description mentioning AA Sequences belongs to a different tag and is ignored per the operations-win rule. - tag: Container spec_file: benchling-container-api-openapi.yml capability_id: BC-1500.60 capability_id_l1: BC-1500 capability_name: Compound & Library Management confidence: 0.7 evidence: '"A Container is a physical vessel (such as a tube, vial, or cryotube) that holds biological or chemical samples in Benchling''s inventory system... Containers support checkout tracking"' reason: Operations create, update, transfer contents between and adjust concentrations of physical sample vessels tracked with barcodes and storage locations — sample/compound repository management in an R&D lab. A generic inventory reading is possible, hence 0.7 rather than higher. - tag: Containers spec_file: benchling-containers-api-openapi.yml capability_id: BC-1500.60 capability_id_l1: BC-1500 capability_name: Compound & Library Management confidence: 0.7 evidence: '"POST /containers/{destination_container_id}:transfer transferIntoContainer Transfer into container"; "GET /containers/{container_id}/contents listContainerContents List a container''s contents"' reason: CRUD, bulk operations, content management and transfers over laboratory sample containers — physical sample/compound repository handling. Title reference to AA Sequences belongs to another tag and is disregarded. - tag: Entries spec_file: benchling-entries-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.7 evidence: '"POST /entries createEntry Create a notebook entry", "GET /entry-templates listEntryTemplates List entry templates"' reason: Electronic lab notebook entries record experimental work, which maps to Experimentation & Prototyping (lab work) under R&D Management. Title mentions AA Sequences but every operation is on notebook entries and templates. recovered_from: sweep-20260828T235257Z-edges.json - tag: Entry spec_file: benchling-entry-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.7 evidence: '"An Entry is the core document type in Benchling''s Electronic Lab Notebook (ELN), used by scientists to record experimental work and observations"' reason: Explicitly the ELN record of experimental work, with authorship and review workflows — this is laboratory experimentation record-keeping under R&D Management. Sub-capability choice (Experimentation & Prototyping vs Research Management) carries some ambiguity. - tag: GroupMembership spec_file: benchling-groupmembership-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.7 evidence: '"Indicates that a Principal is a member of Group. Role indicates that the Principal is a member of a subgroup, such as Admins of the Group. Teams are the canonical example of a Group." with schemas GroupMembership, Group, Team, PrincipalRef' reason: Exposes principal-to-group membership and roles — identity and access administration, not HR org management (no employee lifecycle data). - tag: Locations spec_file: benchling-locations-api-openapi.yml capability_id: BC-530 capability_id_l1: BC-530 capability_name: Inventory Management confidence: 0.7 evidence: operations "List locations", "Create a location", "Archive locations" with schemas LocationsPaginatedList, LocationsArchivalChange reason: Despite the misleading title ('AA Sequences Locations API'), the operations manage inventory storage locations (same Location resource as the other Location tag), which is stock/inventory location administration. L2 left null as the surface is generic CRUD over locations. recovered_from: sweep-20260828T235257Z-edges.json - tag: MatrixPlate spec_file: benchling-matrixplate-api-openapi.yml capability_id: BC-530 capability_id_l1: BC-530 capability_name: Inventory Management confidence: 0.7 evidence: '"A MatrixPlate is a rack-style storage plate where Containers (tubes, vials) can be inserted into and removed from grid positions" ... "MatrixPlates can be stored in Locations, associated with Studies, and identified by barcode"' reason: Operations manage physical sample-storage plates with capacity tracking and placement in locations — inventory holding/storage management of lab materials. Only L1 asserted since no sub-capability matches container-level storage. recovered_from: sweep-20260828T235257Z-edges.json - tag: Procedure spec_file: benchling-procedure-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.7 evidence: '"A reusable template that defines a structured experimental workflow. Procedures specify a sequence of method steps... that scientists follow when running experiments... the procedureType determines whether this is a recipe (synthesis/production workflow) or an assay (analytical workflow)."' reason: Definition and versioning of experimental protocols executed by scientists — laboratory experimentation under R&D Management. Not generic business process modelling, since the artefacts are assays/recipes for lab experiments. recovered_from: sweep-20260828T235257Z-edges.json - tag: ProcedureParameterPlannedValue spec_file: benchling-procedureparameterplannedvalue-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.7 evidence: '"Stores the expected or planned value for a parameter, set during procedure setup or run planning ... the target concentration for a reagent, the expected sample to use, or the equipment to employ"' reason: Planning of experimental parameter inputs before lab execution — part of R&D experimentation/lab work rather than any commercial or manufacturing capability. - tag: ProcedureStepExecutionInstance spec_file: benchling-procedurestepexecutioninstance-api-openapi.yml capability_id: BC-810.30 capability_id_l1: BC-810 capability_name: Experimentation & Prototyping Management confidence: 0.7 evidence: '"representing a step where scientists can document their work ... links to a `Document` (entry) where scientists write notes, observations, and results during execution"' reason: Electronic lab notebook step execution where experimental observations and results are recorded — lab experimentation work. - tag: ServicePrincipal spec_file: benchling-serviceprincipal-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.7 evidence: '"Represents a non-human identity used for system integrations and automated processes" ... "identity for service accounts that perform actions via APIs"' reason: Read-only management of service-account identities used for attribution and auditing maps to Identity & Access Management. Confidence moderated because the surface is only list/get of principals rather than full access administration. - tag: Teams spec_file: benchling-teams-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.7 evidence: POST /teams/{team_id}/memberships "Create team membership"; DELETE "Delete team membership by user ID and team ID" reason: Full CRUD over teams and user memberships is access-group administration (IAM). The OpenAPI title mentioning AA Sequences belongs to a different tag and was disregarded. - tag: WarehouseCredential spec_file: benchling-warehousecredential-api-openapi.yml capability_id: BC-620.20 capability_id_l1: BC-620 capability_name: Identity & Access Management confidence: 0.7 evidence: '"Credentials can have an optional `expiresAt` date for time-limited access and can be permanently disabled via the `revoked` flag"; "Generates a username and password, provisions the credential in the warehouse, and returns the one-time password"' reason: Lifecycle of database access credentials tied to a user's permissions, including expiry and revocation — credential/access management rather than any business-domain capability. recovered_from: sweep-20260828T235257Z-edges.json