Tool
A Tool entry documents software applications, utilities, or platforms designed to perform specific operations in research or technical workflows. These tools can include anything from data analysis programs to machine learning frameworks and bioinformatics utilities. Accurate documentation ensures that tools are easily discoverable, traceable, and appropriately integrated into research processes.
Why You Should Contribute Tool Entries¶
Contributing tool entries supports collaboration, reproducibility, and innovation by helping researchers and teams discover and use essential software for data analysis, visualization, and processing. Accurate documentation ensures tools are accessible and impactful across projects.
Who Should Be Contributing Tool Entries?¶
- Developers – Share tools to boost adoption and integration.
- Researchers – Document tools for replicability and collaboration.
- Data Scientists – Ensure tools critical to workflows are recorded.
- Project Managers – Maintain visibility of tools used across teams.
- IT and Support Specialists – Provide operational details and support resources.
Download Template¶
You can download the ToolView CSV template to streamline data entry.
Example Data Entry¶
The table below includes sample values to demonstrate proper attribute usage.
| Attribute | Example Value |
|---|---|
| Tool Name | Adobe Photoshop |
| Tool Description | "A photo editing tool with advanced image manipulation features, supporting multiple file formats and layers." |
| Tool Release Date | January 5, 2022 |
| Tool Entity Role | Developer, Maintainer |
| Tool Entity Type | Organization |
| Tool Input Data | DNA Sequence |
| Tool Output Data | Gene ID (NCBI): NM_001282392.1 |
| Tool Grant Number | CA209975 |
| Tool Documentation Url | https://docs.example.com/tool-guide.html |
| Tool Operating System | Windows, MacOS |
| Tool Version | 3.2.1 |
| Tool View | Detail View |
| Tool Pubmed Id | 26760201 |
| Tool License | Apache-2.0 |
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | Examples |
|---|---|---|---|---|---|---|---|
| ToolView_id | Unique row identifier, used as a primary key for record updates. | True | string | None | None | None | ToolView_6749 |
| GrantView Key | Unique GrantView_id foreign key(s) that group the resource with other components, as part of the same grant-associated collection. Please provide multiple values as a comma-separated list. | False | string | None | CA\d{6} | None | |
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| DatasetView Key | Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| PublicationView Key | Unique PublicationView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| Tool Name | Canonical tool name provided by the tool developer or service provider. | True | string | None | None | None | Adobe Photoshop |
| Tool Description | Textual description of the tool. | True | string | None | None | None | This is a Python tool that ... |
| Tool Homepage | Homepage of the software, or some URL that best serves this purpose. | True | string | uri | None | None | https://www.example.com/ |
| Tool Version | Version information (typically a version number) of the software applicable to this entry. | False | string | None | None | None | 3.2.1 |
| Tool Operation | The basic operation(s) performed by this software function. Multiple values permitted, comma separated. | True | string_list | None | None | View | DNA Barcoding |
| Tool Input Data | Type of primary input data. Multiple values permitted, comma separated. | True | string_list | None | None | View | DNA Sequence |
| Tool Output Data | Type of primary output data. Multiple values permitted, comma separated. | True | string_list | None | None | View | Accession, Alignment,Biological Model ID |
| Tool Input Format | Allowed format(s) of the input data. Multiple values permitted, comma separated. | True | string_list | None | None | View | CSV |
| Tool Output Format | Allowed format(s) of the output data. Multiple values permitted, comma separated. | True | string_list | None | None | View | FASTQ |
| Tool Function Note | Concise comment about this function, if not apparent from the software description and EDAM annotations. | False | string | None | None | None | The tool is used to programmatically ... |
| Tool Cmd | Relevant command, command-line fragment, or option for executing this function/running the tool in this mode. | False | string | None | None | None | export GIT_TRACE=1 |
| Tool Type | A type of application software: a discrete software entity can have more than one type. Multiple values permitted, comma separated. | False | string_list | None | None | View | Command-Line Tool |
| Tool Topic | General scientific domain the software serves, or other general category. Multiple values permitted, comma separated. | False | string_list | None | None | View | Bioinformatics |
| Tool Operating System | The operating system supported by a downloadable software package. Multiple values permitted, comma separated. | False | string_list | None | None | View | Linux |
| Tool Language | Name of programming language the software source code was written in. Multiple values permitted, comma separated. | False | string_list | None | None | View | Python |
| Tool License | Software or data usage license. Multiple values permitted, comma separated. | False | string_list | None | None | View | Apache-2.0 |
| Tool Cost | Monetary cost of acquiring the software. | False | string | None | None | View | Commercial |
| Tool Accessibility | Whether there are non-monetary restrictions on accessing an online service. | False | string | None | None | View | Nan |
| Tool Download Url | Link to download (or repo providing a download) for the software. | False | string | uri | None | None | https://example.com/tool-download/version2.0 |
| Tool Download Type | The type of data, information, or system that is obtained when the link is resolved. | False | string | None | None | View | API Specification |
| Tool Download Note | Comment about the download. | False | string | None | None | None | Before downloading this tool, ensure your device has adequate storage space and meets the minimum system requirements. Also, our tools may require specific software or apps to function properly. Please refer to our website for detailed information about the required software. |
| Tool Download Version | Version information (typically a version number) of the software applicable to this download. | False | string | None | None | None | 1.0.3 |
| Tool Documentation Url | Link to documentation on the web for the tool. | False | string | uri | None | None | https://docs.example.com/ |
| Tool Documentation Type | Type of documentation that is linked to. Multiple values permitted, comma separated. | False | string_list | None | None | View | API Documentation |
| Tool Documentation Note | Comment about the documentation. | False | string | None | None | None | This software comes with comprehensive user manuals and FAQs to assist in navigation and troubleshooting. Regular updates to the documentation are provided based on software upgrades. |
| Tool Link Url | A link of some relevance to the software (URL). | False | string | uri | None | None | https://www.example.com/tool-info.html |
| Tool Link Type | The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated. | False | string_list | None | None | View | Social Media |
| Tool Link Note | Comment about the link. | False | string | None | None | None | This tool cannot be accessed without a valid institutional login. |
| Tool Doi | The Digital Object Identifier (DOI) associated with the computational tool. | True | string | uri | None | None | https://doi.org/10.1234/example1 |
| Tool Date Last Modified | The date indicating when the tool's entry was most recently modified or updated, providing a timestamp of the latest changes made to the tool's information. | False | string | date | None | None | 11/04/2021 15:30:45 |
| Tool Release Date | The release date of a product or product model. This can be used to distinguish the exact variant of a product. | True | string | date | None | None | January 5, 2022 |
| Tool Package Dependencies | Specifies the software libraries, frameworks, or other components that a tool or package relies on for its proper functioning. This attribute helps users understand the prerequisites needed for installation and usage of the tool within a given computational environment | False | string_list | None | None | None | Python 3.7 or above, Django 2.2 or above, Postgresql 12.0 or above. |
| Tool Package Dependencies Present | Indicates whether the required package dependencies for tool are present. | True | boolean | None | None | View | True |
| Tool Compute Requirements | Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (examples: DirectX, Java or .NET runtime). | False | string_list | None | None | None | Python, pip, pandas, matplotlib |
| Tool Entity Name | Name of the entities that may be credited | False | string_list | None | None | None | Python, pip |
| Tool Entity Type | Types of entities that may be credited, e.g. ‘Person’. | True | string_list | None | None | View | Person |
| Tool Entity Role | Role performed by entity that is credited, e.g. “Developer” | True | string_list | None | None | View | Developer, Maintainer, Provider, Documentor, Contributor |