NTR: PIPseq, Asteria single-cell RNA-seq, and HIVE CLX

[Jchaffer787]

For new term requests, please provide the following information:

Preferred term label

PIPseq

Asteria scRNA-seq

HIVE CLX

Textual definition

PIPseq: The Fluent BioSciences PIPseq TM V T20 3ʹ Single Cell RNA Kit uses Particle-templated Instant Partitions (PIPs) to combine single cell or nuclei suspensions with barcoded beads to produce sequencing-ready libraries in less than 2 days. https://www.fluentbio.com/products/pipseq-v-t20-3-single-cell-rna-kit/

Asteria scRNA-seq: Scipio bioscience Asteria™ Single-Cell RNA-seq kit is a benchtop solution to prepare single cell 3’ end cDNA libraries from cell suspensions. https://scipio.bio/products/asteria

HIVE CLX: HIVE CLX scRNAseq is a complete solution to create NGS libraries from single cells. It utilizes handheld, single-use HIVE Collectors for gentle cell capture and scalable sample processing. Each HIVE contains a picowell array that is pre-loaded with barcoded capture beads for 3’-transcripts. https://honeycomb.bio/wp-content/uploads/2023/05/HIVE-CLX-appnote.pdf

Suggested parent term

EFO:0010183

Attribution

0000-0003-1653-8449

[jychien]

@zoependlington This is also a ticket for CELLxGENE, in association with:

• https://doi.org/10.1101/2024.06.18.599579
• https://cellxgene.cziscience.com/collections/398e34a9-8736-4b27-a9a7-31a47a67f446

Would be great to be able to get these NTRs into EFO, thank you!

[jychien]

@zoependlington Was wondering if there is any updates on this ticket? Are there any changes in the definitions that you would suggest? Thanks!

[jahilton]

Hey @aleixpuigb ! Please let us know if we can offer any additional information for these 3 term requests.

[aleixpuigb]

Hi @jahilton I will have a look at these terms and get back to you if I need more information. Thank you!

[aleixpuigb]

Hi @jahilton @jychien and @Jchaffer787. I will add the terms 'particle-templated instant partition sequencing' (there's two assays that use PIP-seq as abbreviation, we will include as synonym) and HIVE CLX scRNA-seq solution. While I was adding 'Asteria scRNA-seq kit' I realised that OBI has a term 'assay kit'. I believe this term could be directly requested to them to avoid duplicated terms in the future. Would you be ok with that solution? If it helps for the OBI request, here is the definition I was going to add for this term:

A benchtop single-cell RNA sequencing kit developed by Scipio Bioscience that uses hydrogel technology for instrument-free single-cell analysis.

Edit: On second thoughts, it would also be better to request HIVE CLX scRNA-seq solution to OBI.

[jahilton]

Thanks for reviewing these @aleixpuigb CELLxGENE specifically restricts the "assay" submissions to be EFO terms, so OBI terms won't satisfy the schema requirements. We do recognize that there is plenty of vagueness in the field around what is a "kit" vs "assay" etc. But we were thinking of modeling these similar to the 10x terms (eg 10x 3' v3 [EFO:0009922]) which are technically kits, as well. Do you think that would be possible? Is there a different way to frame the definitions in this manner?

[jamesamcl]

@jahilton

CELLxGENE specifically restricts the "assay" submissions to be EFO terms, so OBI terms won't satisfy the schema requirements.

Does this include terms imported into EFO? Many of the terms in EFO are not in the EFO namespace.

[aleixpuigb]

I will request the addition in OBI and import them into EFO once they are released. EFO is trying to move away from creating new terms if they fall within a domain already covered by an OBO ontology. The term 'particle-templated instant partition sequencing' has been added.

[jahilton]

@jamesamcl CELLxGENE currently only allows EFO terms with the EFO namespace. Thus far, EFO alone has offered us the specificity needed in order to thoroughly describe how the single-cell libraries were generated. OBI only has generic terms for "assay" (eg "single-cell RNA sequencing assay") and the "assay kit" terms are incredibly limited. So we have been able to keep a very tightly-defined schema without needing to add that complexity.

Can you help us understand the logic between adding a term in OBI vs EFO? Fully recognize trying to avoid duplication, but without any of these terms already in OBI, it would seem that they could be added in either ontology. These terms seem much more appropriate for EFO given how similar they are to other EFO terms under "single cell library construction". And again, there aren't any existing OBI terms that are very similar to these. Thus, it appears to us that the requested terms would fall into EFO's domain than OBO's domain. Fully recognizing a bit of grey area here - they could each be considered an "assay kit" used for "single cell library construction", so really appreciate your help!

[aleixpuigb]

Hi @jahilton @jychien and @Jchaffer787. The three terms have been added in EFO. Thank you for your contribution. New term IDs: EFO:0900000 'particle-templated instant partition sequencing' EFO:0900001 'Asteria Single-cell RNA-seq Benchtop Kit' EFO:0900002 'HIVE CLX Single-Cell RNAseq Solution'

[jahilton]

Thanks so much @aleixpuigb !