omnisearch / ncro

Non-Coding RNA Ontology

Non-Coding RNA Ontology (NCRO)

The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, aiming to provide a common set of terms and relations that will facilitate the curation, analysis, exchange, sharing, and management of ncRNA structural, functional, and sequence data. Domain includes both natural and engineered RNA.

Current released version will always be available at http://purl.obolibrary.org/obo/ncro.owl (note there is no released version at the moment)

Development HEAD at http://purl.obolibrary.org/obo/ncro/dev/ncro.owl

ncro's Issues

Fix ability to post to google groups

Jinshan and Harrison can't post to google groups - the message is "Web posting has been disabled for this member by their domain administrator"

The issue is described here: https://productforums.google.com/forum/#!topic/apps/rJBQjCEP3CE

Jingshan or delegate needs to talk to their google apps for business admin and have them follow the instructions described in the above referenced discussion.

OBO Version

It is much more urgent to handle the missing NCRO in OBO, because the journal to which we are gonna submit our paper pays a lot emphasis on the Web link of our ontology. Can you manage to get the NCRO back to OBO in the first place? - Jinshan

The "stand-alone" ncro.owl file

Alan: Can u verify the following?

The file accessible at http://purl.obolibary.org/obo/ncro.owl needs to be a stand-alone one, merging all relevant individual owl files into a single owl file. Otherwise, if a user only downloads the ncro.owl file alone, it will not work correctly in Protege by itself.

If this is true, we need to make sure that the ncro.owl file is a correctly merged one before the paper submission.

high-level terms in paper

Guy: There are a total of five placeholders (high-level terms) described in our paper: ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), and small interfering RNA (siRNA). When you edit NCRO, please add them as direct children of the term “ncRNA.” Thanks!

Jingshan

Issues discussed in status update

This is from a discussion thread. Putting them here so they are easy to find. Should probably split into separate issues.

AR We have to figure out what to do about SO.

JH See comments below.

AR figure out what to do with unused, non-reference terms.

JH Make them obsolete terms?

AR Fix where ncRNA goes. Currently it is a sequence feature under mature transcript. But sequence features aren't material entities and ncRNA is.

JH There is an unpublished version of SO (molecular SO) where ncRNA is defined as material_entities. Discussed with Karen earlier, a temporary solution is to place the current ncRNA underneath material_entities and later on switch to the correct ncRNA (in molecular SO).

AR Moreover ncRNA is under mature transcript, but aren't there mature and immature e.g. miRNA?

JH As far as I understand, immature miRNA has another name (something like pri miRNA). We may not need to worry about this b/c we have not utilized, and most likely will not utilize, such pri miRNA.

AR Organize the hierarchy below ncRNA

JH How about keeping the current structure of small_regulatory_ncRNA and adding other high-level place holders like ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), and small interfering RNA (siRNA)?

AR Review other content.
e.g. assertion that Every miRNA has_predicted_target some gene. I don't think that's necessarily true.

JH Discussed earlier with some biologists and got different opinions. Maybe leave it for right now?

Untangle biogenesis- vs function- based definitions

As discussed in [1]
I don't think we have to choose one or the other, but care is needed to avoid asserted multiple inheritance.

[1] Desvignes, T., Batzel, P., Berezikov, E., Eilbeck, K., Eppig, J. T., McAndrews, M. S., et al. (2015). miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends in Genetics, 31(11), 613–626. http://doi.org/10.1016/j.tig.2015.09.002

Add mirtrons

Westholm, J. O., & Lai, E. C. (2011). Mirtrons: microRNA biogenesis via splicing. Biochimie, 93(11), 1897–1904. http://doi.org/10.1016/j.biochi.2011.06.017

Undefined domain-specific relations

The following relations do not have textual definitions. Some seem obvious by their labels, but I never trust that. I'll be trying to define these based on the paper and citation tracking, but contributions are welcome.

The one I was particularly unclear of was is_about_grouped_miRNA. Tracking this down.

hsa-mir-16-1

community annotation: (taken from wikipedia)

The miR-16 microRNA precursor family is a group of related small non-coding RNA genes that regulates gene expression. miR-16, miR-15, mir-195 and miR-457 are related microRNA precursor sequences from the mir-15 gene family.

This is documentation for a family. I presume the family is the one linked to by the "Gene Family" entry on that page.

Wikipedia defines gene family as follows:

A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions.

I speculate that "grouped" miRNA is meant to mean that the group is formed by membership in a gene family, with the source being mirBase.

Please confirm.

If so, then it makes sense that the family would be a class in the same sense as PRO's "Family level distinction"

is_classified_into_gene_family_group
is_gene_template_of_mRNA
is_predicted_target_of
mirRNA_expressed_in_tissue
is_model_of_disease
is_about_mirRNA
is_about_mirRNA_target_gene
is_about_grouped_miRNA
has_predicted_target

New ncro.owl first draft issues

From Darren:

Took a quick look to see if anything jumps out. Consider the following:

1. I notice that the NCBITaxon class 'Mammalia' is placed directly under
   the root term 'Thing' while other such classes are placed under
   'organism'. I presume the latter are PRO imports, since we consider each
   member of a taxonomic group to be an organism. Whichever way is done in
   NCRO, it should be consistent.

2. Some of the miRNA family terms have multiple definitions; for example
   'miRNA family (let-7)'.

3. The family terms indicate chromosome and position. It might not be an
   issue for human cases, but I would caution against stating information
   that can be subject to change if it is not necessary for the definition.

protein_miRNA_promoter_binding

protein_miRNA_promoter_binding is asserted as a subclass of binding, which is a subclass of function.
The logical definition says: protein_miRNA_promoter_binding subClassOf (precedes some miRNA_transcription_initiation)

If I understanding correctly, precedes is a relation used between processes.
http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/BFO_0000063

It can not be used in this case.

What's the relation between CL: cell and PRO: protein

Current design is PRO:protein -BFO2:occurs_in-CL:cell, which is not correct.

review of ncro

1. "cell" needs to be imported from CL (0000000) rather than GO (0005623).
2. "derived_into" and "has_agent" have "#" in their URIs.
3. ontology-metadata.owl appears in both Direct and Indirect Imports in Protege.
4. Is it time-consuming to add "id" annotation for NCRO terms? Especially, those terms at higher levels.

This is just a test

I should receive an email as well.

miRNA_gene_family

All the miRNA_gene_family are information artifacts, but they should probably be classes of (material) miRNA, and superclass of their respective (RNA) members. If they are, then the "gene family" is a misnomer - they are really RNA families. If they are really gene families, then they should still be material entities, and the relation of them to the RNA isn't aboutness - it is creation by transcription.

Check in sakai latest version of ontology then stop using sakai

Check it in with the name "ncro.owl" - github remembers when

relation IAO_0000136 shows only URI without any information.

Need to import this term from IAO.

contributor is not complete

All the people who contributed to the ontology should be named there.
Currently, only two people are listed.

miRNA subclassOf miRNA_expressed_in_tissue some tissue

This axiom isn't true, as miRNA can be expressed in bacteria that are not part of or located in any tissue.

Fix the doid-imports.owl

(1) Add three classes, "disease" (http://purl.obolibrary.org/obo/DOID_4), "disease of cellular proliferation" (http://purl.obolibrary.org/obo/DOID_14566), and "cancer" (http://purl.obolibrary.org/obo/DOID_162), into the doid-imports.owl.

(2) Remove the error message in the doid-imports.owl file: "At least one lower level term IRI is required."

(3) In protege, change the "TEMP" to "doi" in the import list of ncro.owl.

Figure out what our authoritative source(s) for miRNA entities will be

We are using miRBase now. Should we change or augment?

List of miRNAs to add to NCRO ontology

A list of miRNAs that need to be added to the NCRO ontology can be found here:
https://github.com/OmniSearch/omit/blob/master/src/ontology/mirna-to-add.txt

miRNA related processes, functions, complexes

Review GO and gather relevant terms based on discussion in [1], requesting GO terms as necessary and use to help define miRNA related terms in NCRO

[1] Desvignes, T., Batzel, P., Berezikov, E., Eilbeck, K., Eppig, J. T., McAndrews, M. S., et al. (2015). miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends in Genetics, 31(11), 613–626. http://doi.org/10.1016/j.tig.2015.09.002

Possible errors in current NCRO

The list below was created by doing a query on NCRO subclasses of miRNA. In each case that the term had a dbxref, the current label(s) in miRBase version 21 were looked up. When there was any mismatch, I printed the miRBase accession, the current labels in miRBase, the current NCRO label, and the accession looked up in miRBase, for the NCRO label.

I'm not sure what the curation process was earlier, but I suspect, from the look of them, that they are typos, or perhaps in some cases splits (a single entry in miRBase is split into 2).

Before I correct these, I wanted a sanity check from someone.

The function is check-ncro-mirna-against-mirbase in mirbase.lisp

Accession    miRBase labels          NCRO label  Accession from NCRO label
MI0023561   hsa-mir-3690-2          hsa-mir-369 MI0000777
MI0015980   hsa-mir-1302-11         hsa-mir-1302-1  MI0006362
MI0022217   hsa-mir-6505            hsa-mir-650 MI0003665
MI0021274   hsa-mir-6129            hsa-mir-612 MI0003625
MI0025513   hsa-mir-6516            hsa-mir-651 MI0003666
MI0019304   hsa-mir-5697            hsa-mir-569 MI0003576
MI0019140   hsa-mir-5583-2          hsa-mir-558 MI0003564
MI0003592   hsa-mir-585         non_mammalian_miRNA NIL
MI0029321   hsa-mir-548bb           hsa-mir-548b    MI0003596
MI0019114   hsa-mir-4524b           hsa-mir-452 MI0001733
MI0019593   hsa-mir-5701-2          hsa-mir-570 MI0003577
MI0017297   hsa-mir-4667            hsa-mir-466 MI0014157
MI0016833   hsa-mir-548x-2          hsa-mir-548x    MI0014244
MI0022548   hsa-mir-6715a           hsa-mir-671 MI0003760
MI0019293   hsa-mir-5681b           hsa-mir-568 MI0003574
MI0005761   hsa-mir-939         hsa-mir-93  MI0000095
MI0006318   hsa-mir-1228            hsa-mir-122 MI0000442
MI0015977   hsa-mir-1972-2          hsa-mir-197 MI0000239
MI0017320   hsa-mir-1343            hsa-mir-134 MI0000474
MI0014197   hsa-mir-1260b           hsa-mir-126 MI0000471
MI0008195   hsa-mir-1827            hsa-mir-182 MI0000272
MI0016849   hsa-mir-4488            hsa-mir-448 MI0001637
MI0031514   hsa-mir-3670-4          hsa-mir-367 MI0000775
MI0015983   hsa-mir-4315-2          hsa-mir-431 MI0001721
MI0016008   hsa-mir-3618            hsa-mir-361 MI0000760
MI0016014   hsa-mir-3622b           hsa-mir-362 MI0000762
MI0008336   hsa-mir-1915            hsa-mir-191 MI0000465
MI0023563   hsa-mir-6089-2          hsa-mir-608 MI0003621
MI0010633   hsa-mir-2114            hsa-mir-211 MI0000287
MI0017299   hsa-mir-2964a;hsa-mir-219b          hsa-mir-21  MI0000077
MI0011285   hsa-mir-2278            hsa-mir-22  MI0000078
MI0013006   hsa-mir-2861            hsa-mir-28  MI0000086
MI0021279   hsa-mir-6134            hsa-mir-613 MI0003626
MI0024976   hsa-mir-7641-2          hsa-mir-764 MI0003944
MI0031510   hsa-mir-3179-4          hsa-mir-31  MI0000089
MI0006657   hsa-mir-1324            hsa-mir-132 MI0000449
MI0014253   hsa-mir-3202-2          hsa-mir-32  MI0000090
MI0018003   hsa-mir-1273g           hsa-mir-127 MI0000472

Four quick fixes in ncro.owl

(1)
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ncro-obo-WorkingVersion-06302015.owl#"
needs to be changed to:
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ncro.owl#"

(2)
xml:base="http://purl.obolibrary.org/obo/ncro-obo-WorkingVersion-06302015.owl"
needs to be changed to:
xml:base="http://purl.obolibrary.org/obo/ncro.owl"

(3)

needs to be changed to:

(4)
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/ncro-obo-WorkingVersion-06302015.owl#IAO_0000117"/>
needs to be changed to:
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>

BTW, a quick question: the ncro.owl file contains a non-existing URL (http://purl.obolibrary.org/obo/ncro-obo-WorkingVersion-06302015.owl), why it can still be opened in Protege without errors?

OBI_0100047 appears in NCRO without any information

No labels, no definition, etc. in the ontology.
http://purl.obolibrary.org/obo/OBI_0100047

Add Y RNA

Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Letters, 586(8), 1226–1230. http://doi.org/10.1016/j.febslet.2012.03.026

Merge NCRO-Ontology-Design into this one, delete it, and rename this one simply "ncro"

In doing so create usual dev tree

src
ontology
tools
docs
releases

Ontology purl should be fixed

see OBOFoundry/OBOFoundry.github.io#190

You have this registered for auto-builds in OBO:
http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl

But the actual URL for the ontology doesn't match this.

Your release purl should be http://purl.obolibrary.org/obo/ncro.owl, and you should point to the source for the release purl for the OBO build. Note you don't need to specify build information if you are taking care of your own releases.

Let me know if you need help.

ChEBI term requests

ChEBI already has snRNA, circRNA, tRNA, rRNA. I requested they add miRNA, siRNA, lncRNA

https://sourceforge.net/p/chebi/curator-requests/2494/

Once done we should use their terms.

Should tissue be child of 'object aggregate'?

I think tissue maybe just child of 'anatomical structure'.

Add post-transcriptionally modified miRNA isomiRs

Cloonan, N., Wani, S., Xu, Q., Gu, J., Lea, K., Heater, S., et al. (2011). MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biology, 12(12), R126. http://doi.org/10.1186/gb-2011-12-12-r126

this is a test

Inaccurate "Number of Terms" and "Detailed Statistics" on Ontobee

Alan: Both "Number of Terms (including imported terms)" and "Detailed Statistics" on Ontobee provide inaccurate information for ncro (and omit as well). Any idea how to fix this issue?

Why miRNA_and_target_gene_binding is a function?

If it is a function, please change the label to binding function.
Binding is misleading. It sounds as a process term.

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

Sequence ontology miRNA terms

Work with Karen to review/understand relevant terms in SO, relating them to NCRO terms.

Add vault RNA

http://m.mbe.oxfordjournals.org/content/26/9/1975.full.pdf

Telomerase RNA component

https://en.wikipedia.org/wiki/Telomerase_RNA_component