Research_Supplies
BugReporting
Document_Generation
Tutorials
Programmatic_Access
Testing_Tools
State_Funding_Resource
Various spatial and frequency-type data transformations
Spectral_Transforms
Calculation_of_Solvent_Accessible_Area
Hardware_Instrumentation
Describes any kind of measurement designed to describe a phenotype
Phenotypic_measurement
Resource_Integration_Components
Fourier_Transform
Multi-dimensional Fourier transform
These classes may not be needed and could be deleted. They should be reviewed before deleting them.
Image_Processing
Tools and algorithms for dealing with (hyper)images:
Hyper-Volumes / Solids
Intensity-based Solids
Real-valued Intensity-based Solids
* 2D ROIs
* 3D ball-like solids
* 4D time-dependent hyper-volumes
Vector-valued Intensity-based Solids
* 2D ROIs
* 3D ball-like solids
* 4D time-dependent hyper-volumes
Tensor-valued Intensity-based Solids
* 2D ROIs
* 3D ball-like solids
* 4D time-dependent hyper-volumes
Masks of Solids
Deterministic (Binary) Masks
* 2D ROI masks
* 3D ball-like masks
* 4D time-dependent hyper-masks
Probabilistic (Fuzzy) Masks
* 2D ROI fuzzy masks
* 3D ball-like fuzzy masks
* 4D time-dependent fuzzy hyper-masks
Skull_Stripping
Methods for removing of segments from images, which have no valuable information about the biological object. For example, removing non-brain tissue from whole-brain MRI scans, for the purpose of doing quantitative evaluations of time or space changing brain anatomy.
Software designed for interactive use, editors, development tools, etc.
Shape_Analysis
Tools for representation, modeling, analysis and visualization of biological shape:
Points
* Points in Rn
Lines
* Sulci - lines with boundary (homeomorphic to a point)
* UCFs - lines without boundaries (simple-closed contours)
Surfaces
* Patches with boundary (e.g., gyri, sulcal-ribbons)
* Genus-zero surfaces ~ S2 (e.g., cortex, hippocampus)
* Higher-genus surfaces (e.g., tori)
Hyper-Surfaces
* Tunnels (e.g., fMRI time-activation surface map)
ContactModeling
Grid_Computing_Resources
Biomedical_Supplies
Source_Control
EDA
Exploratory data analysis methods.
These are Integration and interoperability tools that valilitate communication between software tools via graphical workflow pipelines.
Graphical_Processing_Workflow_Environments
Methods for co-registration, alignment and warping of imaging and hyper-imaiging data.
Registration
MonteCarloSimulation
Controllers
Toolkit
Refers to any software delivered in toolkit fashion, whereby the kit components can be used independently of each other, or included as part of another program
Phenotype
Refers to any kind of manifestation of a gene or collection of genes
Mechanical_Simulation
Sequence_Similarity_Searching
Any kind of similarity searching involving biological sequences
Self-contained lools, resources and packages for statistical modeling and data analysis (e.g., R, SOCR, SAS, SPSS, SYSTAT, etc.)
Statistical_Package
NumericalIntegrators
Inhomogeneity_Correction
Methods for correction of image intensities where non-biological and non-psysiological drift or noise is introduced by the scanning hardware.
thing stores data
Data_Storage
Regulatory_Signaling_network_reconstruction
PDESolvers
Sources of funding, support materials, documents, private, state and federal agencies, etc.
Funding_Resource
Private_Funding_Resource
Numerical_Calculation_of_Electrostatic_Potential
Methods for automated analysis of object features and quantitative characterization.
Feature_Analysis
General (hyper)volume visualization tools (e.g., volume rendering).
Manifold_Viewers_2D__3D__4D__ND
Resources that are disseminated on the Internet via HTTP, FTP and other web protocols.
Web_Posting
Tools for classification of images and image segmentation.
Segmentation
RootFinders
Cross-Sectional_Viewers
Data visualization tools relying on displays of lower-dimensional cross-sectional (hyper)planes.
Data_Transfer
refers to any documentation describing software
Software_documentation
Any kind of interaction modeling
Interaction_Modeling
General image pre-processing routines that are required as preliminary steps before standard image processing, analysis and visualization take place.
Pre-Processing
Any kind of biological concept or notion
BiologicalConcept
Ontology Development and Management
Data Resources:
* Raw Data - acquired data, going in various SW tools (e.g., NCBI Databases, CCB IDA)
* Model Data - processed data coming out of SW tools (e.g., CCB Atlases)
* Textual Data - spread sheets, web-pages (e.g., Imaging Glossary)
* Data Types
o XML (e.g., Module Descriptions)
o JSON Objects - language independent, data transfer, data attributes (e.g., JSON output from the Yahoo! Web Services contain the same data as an XML object; the only difference is in the format, Get GeoNames PostalCodes within 10-miles of US 90095)
o Binary Data (e.g., CCB IDA)
o Comma-separated-values, .csv (e.g., California Department fo Water & Power)
Data_Resource
Bibliographic_Resource
Web_Access
Natural_Language_Processing
Resource
Individual, self-contained and atomic software tools or libraries that are invoked by the user on local machines or remote servers.
# Computational Algorithms (e.g., Level-sets, Bioinformatics Algorithms)
# Software Suites (e.g., Vista, geWorkbench, FEATURE, ShapeViewer, Slicer3D, Pipeline)
# Dowloadable libraries (e.g., ITK, ShapeToolsLibrary)
# Locally Executable programs (e.g., Debabeler, )
Structure information resource including an ontology and instance data
Describes any kind of measurement, whether in pre-clinical experiments or obtained in a clinical trial in the life sciences
Measurement
Research intended to progress from laboratory knowledge to knowledge that impacts health (human, animal or plant)
TranslationalResearch
Clinical_data
Any type of data obtained in the course of caring for humans outside of measurements obtained in clinical trials
Cross-Language_Wrapping
Cross-Platform_Tools
These are resources that allow tool interoperability and resource integration and data mediation.
Integration_and_Interoperability_Tools
Genomic___Phenotypic_Analysis
Network_characterization
Tools for graphical, interactive, multimodal and multidimensional data and result visualization.
Visualization
Filtering
General image filtering methods
Homology_Modeling
Ontology_Diff_and_Alignment
Multi-dimensional wavelet transform
Wavelet_Transform
Individual_Human_Data
Any kind of software used in simulations if random events, biological structures, kinetics, function, structure, genotype of phenotype in time and space.
Simulation
Educational resources (incl. book, magazines, audio, video, digital streams, etc.)
Education
Cross-LanguageWrapping
Algorithms applied to networks and graph data structures
Sequences
Molecular sequence viewers
Molecular_Interaction
Applies to any kind of experimental measurement of interaction between molecules of any type
Molecular_Visualization_Package
Paper
Sequence_Annotation
Optimizers
Random_Number_Simulation
Stochastic_Simulation
Simulations, sampling and resampling methods for random events.
Structure-based_protein_classification
General numerical modeling and computational tools (ala, GAMS: http://gams.nist.gov/)
Numerical_Methods
Nonhuman_Data
MultibodyDynamics
Course_Material
Resources for data management, retrieval, query, transfer and mapping.
Data_Management
BasicResearch
purpose of thing is basic research defined as...
Interactive_Web-Based_Tool
Interactive hands-on resources for data management (entry, query, traversal, comparison, etc.)
Viewers of directed, acyclic tree-structures.
Hierarchical_Trees
Mappers_e.g.__BrainGraph_BrainMapper
Analytical
Modeling and computational methods that have closed-form analytical mathematical representations.
Molecular_Modeling_and_Classification
Tools for computational geometric representation and analysis.
Computational_Geometry
Ontology_Visualization
LinearAlgebraTools
Data_Transforms
General data transformations
Ontology_Development
Protein_interaction_modeling
Information_retrieval__traversal_and_querying
Imaging
Visualization tools for (hyper)imaging data.
Publication
Software_Engineering_and_Development_Tool
Generic tools for software development, engineering and deployment.
Image
Applies to any kind of image data obtained from an instrument or generated through computational extrapolation
FeatureRequest
purpose of thing is clinical research defined as ...
ClinicalResearch
Pattern_Recognition
Mehtods for pattern recognition and analysis.
In what area of research is this object used?
AreaOfApplication
White_Paper
Integration
Portals
Sparse matrix representations of networks
Root concept for any kind of document
Document
Cloud computing
A general type of algorithmic resource.
**previously was called Clinical_Charts_eg_Demographics
we think this should be deleted
Support
Federal_Funding_Resource
Graph_Viewers
General graph visualization resources
Atlas_Generation
Techniques for construction of new computaitonal atlases of biological objects using imaging techniques.
used to be eg__HIVE_Pipeline
Cortical_Modeling
Detection, extraction, representation and analysis of cortical brain structure.
Prediction_of_Side-chain_Conformations
Community and User Interaction Systems, educational resources and web-services.
Dissemination_Vehicle
Online training and educational resources.
OnlineCourse
News
News and RSS feed resources
Aggregate_Human_Data
3-D models evolving in time
Software_Technology_Protocol
Meshing
MailingList
Data_Annotation
Biochemical_Supplies
MolecularForceFieldCalculator
Variety of software libraries and tools for statistical modeling and analysis.
Statistical_Analysis
Graphical_Integration
ComputationalGeometry
Ontology
Heterogeneous_Funding_Resource
Hyperbolic_Graphs
Hyperbolic space (hierarchical) graph/tree visualization tools.
Any kind of database where the database constitutes a very significant component of the system
Database
What are the goals of the document
DocumentGoal
Data output
Data input
Resource type
Scientific purpose of algorithm
AlgorithmPurpose
OutputForm
What form of output is produced by this thing
MeasurementType
what kind of information is being capture in this measurement?
InteractionType
What type of interaction is this?
Information about the last release
ProteinType
broad classification of protein type based on structure or function
PeerReviewStatus
is this a peer-reviewed scientific publication?
Other_Information
Description of the resource
Description
Originator of a class
Originator
Implementation Language
Implementation Language(s)
License
Resource authors
Author list
Platforms tested
Platforms tested
choice of either many individual keyword elements or one element with comma-separated-values
Target_User_Type
Organization
Name
Name of the resource
Development stage
e.g., beta, production
Identifier
Any kind of identifier
Version number
Version Number
Implementation_Language
TranscriptType
Type of biological transcript