Terms and Conditions (version 2)

Revised October 2022

Version 2 changes

  • Updated policy on prohibited use to clarify human vs human microbiome data, and the requirement for human microbiome data to be collected under IRB-approved protocol.
  • Added statement to inform users that KBase is managed by and also subject to Lawrence Berkeley National Lab’s privacy policy.
  • Added policy on data reuse. In brief, all data remains private until a user shares with individual(s), organization(s), or makes a Narrative public. Sharing a Narrative within the KBase platform grants fair use but should be accompanied by full credit and attribution in all derived works. If a user creates a Static Narrative and requests a DOI, the default license applied is Creative Commons Public Domain (CC0) or the user can request a Creative Commons with Attribution (CC-BY-4.0) license. Review the Data Policy section for full details.
  • Added National Microbiome Data Collaborative and Protein Data Bank as data sources. Updated JGI data license to link to their policy site.

Version 1

KBASE USE AGREEMENT

By using KBase, including its websites and services or via published APIs, you are agreeing to the terms stated below. Please read them carefully. They include limitations on what is acceptable user behavior, accountability, availability, data retention, and conditions for account termination. If you do not agree, do not access or use KBase.

Acceptable use

Do not misuse KBase. For example, do not interfere with services or try to access them using a method other than the interface and the instructions provided by KBase. You may use KBase and its services only as permitted by law, including applicable export and re-export control laws and regulations.

You agree not to use KBase to submit, upload, post email, transmit, or otherwise make available any user content that is unlawful, harmful, threatening, abusive, menacing, harassing, tortious, defamatory, vulgar, pornographic, obscene, offensive, blasphemous, libelous, unlawful, invasive of another’s privacy or publicity rights, hateful, or racially, ethnically or otherwise objectionable.

Your account may be suspended if you do not comply with the terms and policies in this Agreement, or while suspected misconduct is being investigated.

Prohibited use

Do not upload any type of human data, personally identifiable information, or restricted data.

As a condition of your use of KBase (the DOE Systems Biology Knowledgebase) you agree not to upload any type of human data or personally identifiable information. KBase requires any user uploading data associated with human subjects (i.e., “human microbiome”) to verify in writing inside a Narrative markdown cell that 1) the user is an authorized contact for these data and authorized to submit, share or release these data; 2) the data were collected under an IRB-approved protocol (including the IRB protocol number); and 3) that the data were stripped of identifiers that could link the data to the individual from whom it was collected, prior to uploading to KBase.

Any individual who accesses these data sets commits that they will not attempt to re-identify the data. If individually identifiable data are found inside KBase, contact engage@kbase.us immediately.

Other prohibited data include data that are export controlled, categorized as “Official Use Only” or “Controlled Unclassified Information” by the US Government, or any other data that the data owner would classify as “Moderate” or “High” under Federal Information Processing Standards (FIPS) Publication 199: Standards for Security Categorization of Federal Information and Information Systems.

WARNING: Improper use of KBase, including uploading human data, may result in the termination of KBase access privileges.

KBase User Account

You will need a KBase Account to use some of the KBase services and may create this via the Sign Up process on www.kbase.us. You are responsible for maintaining the confidentiality of account information (i.e., username and password) that you use to access KBase, and for signing out of your account.

To protect your account and personal information, you agree to keep your password confidential. You are responsible for all activity that happens on or through your account. Do not share information for the account you use to sign into KBase. You are responsible for maintaining appropriate security measures.

If you learn of any unauthorized use of your KBase account, you agree to immediately contact KBase. KBase will not be liable for any loss or damage arising from your failure to comply with this guidance.

Termination of KBase User Account

Rights granted to you herein will terminate immediately upon violation by you of this Agreement. KBase at its sole discretion reserves the right to temporarily or permanently terminate your access to and use of KBase at any time and for any reason whatsoever without notice or liability. KBase will not be liable to you or any third party for any termination.

Warranty Disclaimer

KBase is provided “AS-IS,” without warranty of any kind, either express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose, and non-infringement. Your use of KBase is at your own risk.

Limitation of Liability

You acknowledge and agree that KBase will not be responsible for any damages to you or to any third party including for direct, indirect, special, incidental, consequential or punitive damages arising out of or in connection with this Agreement, or from the use of, or inability to use KBase. In no event shall KBase, its staff, developers, contributors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the KBase system or software or its use or other dealings in the software.

Changes to Use Agreement

This KBase Use Agreement may change from time to time. Your rights under this agreement will not be reduced without your explicit consent. Changes will be posted on this page, and if significant, will be provided more prominently via email or notification when you sign in.

Users may at any time review, update or delete the personal information in their profiles.

PRIVACY POLICY

The DOE Systems Biology Knowledgebase Project (KBase) is provided as a public service. KBase reserves the right to monitor any and all use of kbase.us domains. This Privacy Policy describes the ways KBase collects, stores, uses, discloses and protects the personal information about users and how they use KBase. A direct link to this section of the KBase Terms and Conditions appears in the footer of www.kbase.us webpages and other prominent locations such as the Sign Up page, where it must be acknowledged to obtain a KBase User Account. KBase never collects information for commercial marketing or any purpose unrelated to KBase functions. KBase is managed by and also subject to Lawrence Berkeley National Lab’s privacy policy.

Information KBase collects

Some functions of KBase may be used without a KBase User Account, in which case KBase does collect some information about your visit to the website to help understand how it is used and might be improved. If you choose to have a KBase User Account, you are asked to provide your name and an email address, and we may contact you if needed.

KBase Account Names are not treated as personal information, and it is recommended that you not include personal information in your account name.

User-provided personal information and data

You may, at your discretion, also provide further biographical information in your personal profile, such as a profile image, your real name, education, position, affiliations (both institutional and interpersonal, i.e., colleagues), etc.

KBase does not track information in your personal research data other than to provide indexing to support your searches, and verify that the data and its use adheres to the KBase Use Agreement. Access to this information is strictly under your control to share or make public.

Once data or Narratives are designated as shared or public, you should be aware that other users of KBase will be able to use them. See the data policy section for details.

User behavioral profile

When you visit KBase or use its services, usage information is automatically recorded by your account name including what services you used as well as information such as your computer’s Internet Protocol (IP) address, your browser type and operating system, the web page you were visiting and visit over time on kbase.us domains, information searched for, access times and dates, what resources are consumed (CPU, disk, etc); all acts of creating Narratives and data, sharing Narratives or resources, uploading data files, input and output from KBase services, user input to Narrative cells, input to any future rating systems or ‘liking’, linking to or citing other Narratives, URLs, or references; user comments; and information learned from user activity such as common parameters for services, frequently used services, combinations of services, frequently used datasets, and the number of times a Narrative is copied, cloned, or referenced by others.

How information collected by KBase is used

Private personal information is only accessible to KBase staff and will only be used individually in the event we need to contact you. If you choose to provide that information to KBase independently (for example when emailing to request help), again it will only be used by KBase staff for the purpose of responding. KBase will produce project reports that include aggregate information such as the number of help requests, statistics on the topics of requests and resolutions, and analyses of the institutions and types of users such as can be derived from email addresses. Additionally, the ways users interact with the system are analyzed when errors occur and in aggregate for analysis of KBase operation and improvement.

Aggregated usage information based on user behavior is used by KBase to produce overall statistics such as to show users which Apps are most popular. Usage information is also used by KBase for internal purposes such as to manage and improve capabilities and services, the website and related features and content, and to enable users to easily and productively navigate the website and utilize KBase capabilities for research benefit.

Aggregated usage analyses do not link to individual personal information but may include results broken down by aggregated personal information for example geographic region or type of institution.

Users should also understand that once their research data is made public that KBase reserves the right to integrate this information into meta-analyses that the KBase system might perform.

Information KBase discloses

KBase is committed to maintaining the confidentiality, integrity, and security of users’ personal private information and data. KBase considers user data to be private and held in confidence or shared as designated under user control until a user makes it public.

Usage information is used for privately reporting to our funding agency, the Genomic Science Program of the Biological Systems Science Division of the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER), for the purpose of evaluating the performance of the overall project. No individually identifiable information is reported or disclosed.

How information KBase collects is protected

KBase restricts access to nonpublic, personal information (e.g., email address) to those staff and service providers involved in administering and servicing user accounts. Physical, electronic, and procedural safeguards are in place that comply with federal standards to protect such information.

Changes to Privacy Policy

This KBase Privacy Policy may change from time to time. Your rights under this policy will not be reduced without your explicit consent. Changes will be posted on this page, and if significant will be provided more prominently via email or notification when you sign in.

Users may at any time review, update, correct or delete the personal information in their profiles by signing in to their KBase account and using the edit or remove functions available from their personal profile page.

DATA POLICY AND SOURCES

As a community of data scientists (see KBase Code of Conduct), please be respectful and cite all data sources that contribute to your work. If the data are not published, contact the data generator about their policy for use of these data.

Data Policy

KBase conforms to the Information and Data Sharing Policy of the Genomic Science Program of the Office of Biological and Environmental Research within the Office of Science. This requires that all publishable data, metadata, and software resulting from research funded by the Genomic Science program must conform to community-recognized standard formats when they exist, be clearly attributable, and be deposited within a community-recognized public database(s) appropriate for the research.

Data publicly available in KBase comes from the sources listed below. When logged into the KBase platform (https://narrative.kbase.us/), all data are private until a user shares their Narrative(s) with individual KBase users or a KBase Organization, or until a Narrative is made public. A public Narrative in KBase is visible only to other KBase users and is not accessible outside the KBase platform. Narratives shared with the KBase Help Desk are an exception, as those are only used to provide technical support and are not considered shared or public Narratives.

Data sharing within the KBase platform permits reuse of the data to those individuals, Organizations, and all other KBase users. The Narrative owner retains rights that govern the reproduction, redistribution, and re-use of work captured by the Narrative. KBase infrastructure supports attribution by tracking the provenance of data ownership, and provides citation information to allow for appropriate attribution. Any reuse of work contributed by other KBase users must be accompanied by full credit and attribution in all derived works, or the user should seek the permission of the owner(s) when intended activities fall outside reasonable fair use (e.g., for direct commercial profit). Failure to comply may result in the termination of KBase access privileges.

When a KBase user makes a “static” Narrative, it creates an HTML snapshot of the current version of the Narrative and makes it available outside of the KBase platform. The static Narrative is immutable, released to the general public, and indexed and discoverable through search engines. Any reuse of work in the static Narrative requires the individual to log into the KBase platform, and is therefore subject to the same credit and attribution requirements as above.

When a KBase user requests a DOI for a static Narrative, KBase will work with the user to ensure appropriate credit, attribution, and licensing are assigned for all data and software used in the analysis. KBase also provides the user with the option to choose between Creative Commons Public Domain (CC0, default) and Creative Commons with Attribution (CC-BY-4.0, by request) for the static Narrative instance being assigned a DOI. Finally, KBase will provide a full data citation for the static Narrative for use in preprints and publications.

KBase does not release or use private data for any internal analyses, with the exception of collecting metrics on 1) amount of data and 2) the distribution of data types in system, and 3) app usage across system as an aggregate of user activity, and to provide the data owner with additional context for how their private data is related to other data made accessible in KBase. KBase will never expose your private data in any way nor use private data for any publication without a formal collaboration with the data owner(s).

WARNING

Improper use of KBase, including uploading human data, may result in the termination of KBase access privileges. Please see the prohibited use section for more information.

Data Sources

Source License Download

Genomic Data

NCBI RefSeq Public Domain –- US Government FTP
PATRIC Public Domain –- US Government FTP
SEED Public Domain FTP
Phytozome Free (no embargoed/early release genomes) Download (login required)
MycoCosm Free (no embargoed/early release genomes) Download (login required)
Gramene Public Domain FTP
JGI Public Domain –- US Government HTTP (genome portal)
NMDC Creative Commons 4.0 with Attribution HTTP

Ribosomal Data

Greengenes Creative Commons Attribution-ShareAlike 3.0 Unported License HTTP
SILVA Academic/non-commercial HTTP
RDP Creative Commons Attribution-ShareAlike 3.0 Unported License HTTP

Ontologies

GO Creative Commons Attribution 4.0 Unported License HTTP
GSC Unknown HTTP

Pathway Data

KEGG maps Academic license required HTTP
ModelSEED Public Domain –- US Government HTTP

Protein Annotations

UniProt Public Domain HTTP
RAST Public Domain FTP

Structure

Protein Data Bank Public Domain HTTP/FTP

RESPONSIBILITY FOR DATA

As a condition of your use of KBase you accept sole responsibility for all files you upload or transfer through use of KBase. You recognize and accept that KBase does not guarantee long-term retention of user-uploaded data, and will not be responsible for any failure to store or transfer, or deletion, corruption or loss for any data, information or content contained in your files. It is strongly recommended that you backup all files prior to using KBase.

OPEN SOURCE LICENSE

All software developed by the KBase project team, and any contributed by you to KBase, is stored and maintained in the public KBase GitHub code repository under the MIT Open Source License (“License”). By contributing to or using KBase, you acknowledge having read and understood the License and agree to abide by it.

KBASE CITATION

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163.

Funding: This work is supported as part of the BER Genomic Science Program. The DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.