Support & FAQ
Support Description
- Looking for something you can't find here?
If you have questions not covered by the documentation, website, or the following F.A.Q., please contact support@ontology.bio for assistance.
Frequently Asked Questions
Frequently Asked Questions
ONTOLOGY Kits
How long do ONTOLOGY kits last? Is there a warranty?
ONTOLOGY kits are supported under warranty for six months from the date of shipment, so long as they are stored under ideal conditions as defined by the End User License Agreement.
For warranty claims, contact support@ontology.bio.
How should I store my kits?
We recommend storage of kits in the refrigerator at 4°C, where they are stable for at least six months. Kits are stable at room temperature for several weeks (not recommended).
Kits can also be kept in the freezer for long-term storage, though care must be taken to avoid freeze-thaw cycles. If removing kits from freezer for transport at room temperature, move them to a refrigerator for 24 hr beforehand to avoid risk of condensation due to rapid temperature change.
How many plates come in an ONTOLOGY kit?
Presently, all ONTOLOGY kits include 10 plates, each with 96 wells. To inquire about custom orders, please contact orders@ontology.bio.
What laboratory equipment and skills are required to use ONTOLOGY?
ONTOLOGY requires access to a standard molecular laboratory, with equipment to extract DNA, conduct PCR, quantify DNA, prepare DNA for sequencing, and sequence DNA. Presently, ONTOLOGY is optimized for Oxford Nanopore Technologies’ sequencers and flow cells, but experienced users may use .fastq files generated by any long-read sequencer.
ONTOLOGY is designed for use by researchers without advanced training in molecular biology or bioinformatics. Undergraduate-level laboratory experience with standard protocols (PCR, DNA Library Preparation) is recommended and ONTOLOGY provides detailed tutorials to help users gain this experience. If you are familiar with current DNA barcoding or eDNA protocols, you will find the ONTOLOGY protocol more straightforward.
ONTOLOGY Software
What are the system requirements needed to use ONTOLOGY software?
The ONTOLOGY App will be available on macOS, Windows, and Linux at launch. Recommended specifications will be available in September 2026. Users analyzing large sequencing runs (e.g., PromethION) may require more powerful machines.
Do I need to use the ONTOLOGY plates to use the ONTOLOGY software?
No. The ONTOLOGY software supports custom UMIs and primers for advanced users.
Does ONTOLOGY require an internet connection?
ONTOLOGY works entirely offline. If the software is downloaded and you have your reference libraries, you can complete the full workflow. Submission of data to BOLD requires an internet connection.
What Reference Libraries are used by ONTOLOGY?
ONTOLOGY can work with any reference library that is provided in the open-source SINTAX format (.fasta). ONTOLOGY has built-in support for BOLDistilled libraries which can be downloaded from within the App.
Misc.
What markers and taxa are supported by ONTOLOGY?
ONTOLOGY currently only supports the standard animal DNA barcode: COI-5P. We plan to add new plates according to demand. Users can use their own custom UMIs and primers with the software, however. Contact dev@ontology.bio if there is a specific marker you would like to see ONTOLOGY support—we keep track of all requests!
How can I cite ONTOLOGY?
ONTOLOGY must be cited when the plates and/or software are used to generate results.
Please cite the following in-prep manuscript:
Paul DN Hebert, Emine Oszahin, Ken A Thompson, Robin M Floyd, Saeideh Jarfapour, Sean WJ Prosser. ONTOLOGY – Enabling Nanopore Sequencing for DNA Barcoding and Metabarcoding. Manuscript in Prep.
Why is it called ONTOLOGY?
Ontology is the branch of philosophy that aims to discover the basic building blocks of our universe or selected domains of it. Species are the fundamental particles of biological systems, but most are unknown, dark taxa waiting in the taxonomic twilight. Because ONTOLOGY aims to illuminate them, moving unknown to known, it is aptly named.
Are data generated by ONTOLOGY made public?
For ONTOLOGY kits sold at the research rate, we expect data to be made public via upload to BOLD, in accordance with the ONTOLOGY Research Rate Data Agreement. For kits purchased at Standard Rate, data can remain private and upload to BOLD is optional.
How long do ONTOLOGY kits last?
ONTOLOGY kits are supported under warranty for six months from the date of shipment.
How should I store my kits?
We recommend storage of kits in the refrigerator at 4°C, where they are stable for at least six months. Kits are stable at room temperature for several weeks (not recommended).
How many plates will come in an ONTOLOGY kit?
Presently, all ONTOLOGY kits include 10 plates, each with 96 wells.
What laboratory equipment and skills are required to use ONTOLOGY?
ONTOLOGY requires access to a standard molecular laboratory, with equipment to extract DNA, conduct PCR, quantify DNA, prepare DNA for sequencing, and sequence DNA. Presently, ONTOLOGY is optimized for Oxford Nanopore Technologies’ sequencers and flow cells, but experienced users may use .fastq files generated by any long-read sequencer.
ONTOLOGY is designed for use by researchers without advanced training in molecular biology or bioinformatics. Undergraduate-level laboratory experience with standard protocols (PCR, DNA Library Preparation) is recommended and ONTOLOGY provides detailed tutorials to help users gain this experience. If you are familiar with current DNA barcoding or eDNA protocols, you will find the ONTOLOGY protocol more straightforward.
What are the system requirements needed to use ONTOLOGY software?
The ONTOLOGY App will be available on macOS, Windows, and Linux at launch. Recommended specifications will be available in September 2026. Users analyzing large sequencing runs (e.g., PromethION) may require more powerful machines.
Do I need to use the ONTOLOGY plates to use the ONTOLOGY software?
No. The ONTOLOGY software supports custom UMIs and primers for advanced users.
Does ONTOLOGY require an internet connection?
ONTOLOGY works entirely offline. If the software is downloaded and you have your reference libraries, you can complete the full workflow. Submission of data to BOLD requires an internet connection.
What Reference Libraries are used by ONTOLOGY?
ONTOLOGY can work with any reference library that is provided in the open-source SINTAX format (.fasta). ONTOLOGY has built-in support for BOLDistilled libraries which can be downloaded from within the App.
What markers and taxa are supported by ONTOLOGY?
ONTOLOGY currently only supports the standard animal DNA barcode: COI-5P. We plan to add new plates according to demand. Users can use their own custom UMIs and primers with the software, however. Contact dev@ontology.bio if there is a specific marker you would like to see ONTOLOGY support—we keep track of all requests!
How can I cite ONTOLOGY?
Please cite the following in-prep manuscript:
Hebert, PDN*; Oszahin E*, Thompson KA*, Jarfapour S*, Floyd RM*, and SWJ Prosser*. ONTOLOGY: A Standardized, Distributable, and Open-Ended Platform for High-Throughput DNA Barcoding and Metabarcoding. Manuscript in Prep.
Why is it called ONTOLOGY?
In information science an ‘ontology’ is a structured and formal specification of the concepts, categories, and relationships within a domain. ONTOLOGY facilitates the connection of all forms of information commonly used in biodiversity science and DNA-based species identification. It also is a reference to the Biodiversity Institute of Ontario (Canada), where the work that gave rise to ONTOLOGY was first undertaken.
Are data generated by ONTOLOGY made public?
For ONTOLOGY kits sold at the research rate, we expect data to be made public in accordance with the ONTOLOGY Research Rate Data Agreement. For kits purchased at Standard Rate, data can remain private.
Acknowledgements
The development of ONTOLOGY was enabled by grants from the Gordon and Betty Moore Foundation and the government of Canada through Ontario Genomics and Genome Canada.
Additional Resources
ONTOLOGY Manual
The ONTOLOGY manual (COMING SOON) provides details about the software, including a tutorial.
ONTOLOGY Support
Please email support@ontology.bio with any questions you cannot find the answers for on this website.
Bug
Reporting
Email dev@ontology.bio to report bugs or any other issues encountered with the software.