Please add a new term "Cyst". I see there is a term for cyst wall, which would be a part of a cyst. The definition of cyst wall gives a good definition for cyst, but I cannot find a term just for cyst. Am I missing it?
We have ‘cyst wall’ but not ‘cyst’ in GO because the latter falls outside the scope of GO terms (cellular components in this case - a cyst is not a cell substructure):
(from the def of ‘cyst wall’) “…A cyst is a resting or dormant stage of a microorganism, usually a bacterium or a protist or rarely an invertebrate animal, that helps the organism to survive in unfavorable environmental conditions. …”
The Cell Type Ontology (CL), instead, has these terms, for example:
CL:0000724 heterocyst
is_a nitrogen fixing cell, is_a prokaryotic cell
A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
CL:0000722 cystoblast
is_a germ cell
(Not defined further)
Chris, would the def of ‘cyst’ as we refer to it in GO above be good enough for a broad CL term? I came across a similar issue with the Giardia project too. Strictly speaking, they could actually do without a ‘cyst’ term, but I think a general term might be useful to more than just Anne. Or is there an appropriate term in another ontology - looking ‘cyst’ up in Ontobee retrieves a few thousand results…
Thanks,
Paola
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I looked around in Ontobee and I found BTO:0000320. I'm not sure of the quality of this ontology. I don't think either of those two CL terms would work for me. What do you think of the BTO ontology?
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BTO is not fully open (although it's freely available to academics).
BTO often mixes together concepts. For example, BTO:0000320 mixes the cyst wall with the cyst. May not matter for your purposes. In general we have good mappings from BTO to other ontologies, so you may be able to mix and matching.
I think 'microbial cyst' belongs in CL
We could also have a 'cyst stage' in GO or a microbial staging ontology.
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I agree that cyst terms belong in the CL, but need to be distinguished as 'bacterial cyst' or 'protist cyst'. If there is to be a general 'microbial cyst' term, it needs to be defined functionally, since bacterial cysts and protist cysts rely on different structural elements to achieve their function.
-- Alex
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Anne, would you be happy with using BTO:0000320 for your purposes?
Otherwise, you may have to wait for the CL editors to create one or more new terms for cyst types. I made a ticket for that, here:
Chris, a GO term for 'cyst stage' would better refer to appropriate CL term(s), e.g. not to create confusion with existing 'encystment' terms (even though those refer to a process more than a stage/phase strictly speaking). If so, I'll set this ticket to pending while waiting for the CL term(s). Otherwise, is there a microbial staging ontology that you could use?
Thanks,
Paola
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Yes, I will either use the BTO term or wait for the CL term.
a
On 12/17/2014 10:57 AM, Paola Roncaglia wrote:
Hi all, thanks for your feedback.
Anne, would you be happy with using BTO:0000320 for your purposes?
Otherwise, you may have to wait for the CL editors to create one or
more new terms for cyst types. I made a ticket for that, here:
Chris, a GO term for 'cyst stage' would better refer to appropriate CL
term(s), e.g. not to create confusion with existing 'encystment' terms
(even though those refer to a process more than a stage/phase strictly
speaking). If so, I'll set this ticket to pending while waiting for
the CL term(s). Otherwise, is there a microbial staging ontology that
you could use?
Status: open Group: None Labels: New term request Other term-related request Dinoflagellate
cell type Created: Thu Dec 04, 2014 03:34 PM UTC by Anne Last Updated: Fri Dec 12, 2014 01:12 PM UTC Owner: Paola Roncaglia
Please add a new term "Cyst". I see there is a term for cyst wall,
which would be a part of a cyst. The definition of cyst wall gives a
good definition for cyst, but I cannot find a term just for cyst. Am I
missing it?
GO should have specific classes for the the walls of bacterial and protist cysts, especially if these are non-homologous and composed of different structures. We always get into trouble when we force annotation to a generic grouping class.
We also need this since cyst walls for taxon X are not fully classified
is_a GO:0005618 ! cell wall
is_a GO:0009274 ! peptidoglycan-based cell wall <-- bacterial cell wall here?
is_a GO:0009277 ! fungal-type cell wall <-- is this a type of chitin cell wall? like a protozoan cell wall? If so add a composition based grouping
is_a GO:0009505 ! plant-type cell wall
is_a GO:0031160 ! spore wall
is_a GO:0097570 ! cyst wall ***
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Hi Anne,
We have ‘cyst wall’ but not ‘cyst’ in GO because the latter falls outside the scope of GO terms (cellular components in this case - a cyst is not a cell substructure):
(from the def of ‘cyst wall’) “…A cyst is a resting or dormant stage of a microorganism, usually a bacterium or a protist or rarely an invertebrate animal, that helps the organism to survive in unfavorable environmental conditions. …”
The Cell Type Ontology (CL), instead, has these terms, for example:
CL:0000724 heterocyst
is_a nitrogen fixing cell, is_a prokaryotic cell
A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
CL:0000722 cystoblast
is_a germ cell
(Not defined further)
If you’d like to suggest a new cyst-type term to belong in the Cell Type Ontology, you may open a ticket in this tracker:
https://code.google.com/p/cell-ontology/issues/list
Chris, would the def of ‘cyst’ as we refer to it in GO above be good enough for a broad CL term? I came across a similar issue with the Giardia project too. Strictly speaking, they could actually do without a ‘cyst’ term, but I think a general term might be useful to more than just Anne. Or is there an appropriate term in another ontology - looking ‘cyst’ up in Ontobee retrieves a few thousand results…
Thanks,
Paola
I looked around in Ontobee and I found BTO:0000320. I'm not sure of the quality of this ontology. I don't think either of those two CL terms would work for me. What do you think of the BTO ontology?
Not very familiar with it, really. Chris?
BTO is not fully open (although it's freely available to academics).
BTO often mixes together concepts. For example, BTO:0000320 mixes the cyst wall with the cyst. May not matter for your purposes. In general we have good mappings from BTO to other ontologies, so you may be able to mix and matching.
I think 'microbial cyst' belongs in CL
We could also have a 'cyst stage' in GO or a microbial staging ontology.
I agree that cyst terms belong in the CL, but need to be distinguished as 'bacterial cyst' or 'protist cyst'. If there is to be a general 'microbial cyst' term, it needs to be defined functionally, since bacterial cysts and protist cysts rely on different structural elements to achieve their function.
-- Alex
Hi all, thanks for your feedback.
Anne, would you be happy with using BTO:0000320 for your purposes?
Otherwise, you may have to wait for the CL editors to create one or more new terms for cyst types. I made a ticket for that, here:
https://code.google.com/p/cell-ontology/issues/detail?id=162&start=100
Chris, a GO term for 'cyst stage' would better refer to appropriate CL term(s), e.g. not to create confusion with existing 'encystment' terms (even though those refer to a process more than a stage/phase strictly speaking). If so, I'll set this ticket to pending while waiting for the CL term(s). Otherwise, is there a microbial staging ontology that you could use?
Thanks,
Paola
Yes, I will either use the BTO term or wait for the CL term.
a
On 12/17/2014 10:57 AM, Paola Roncaglia wrote:
--
Anne E. Thessen, Ph.D.
The Data Detektiv, Owner and Founder
Ronin Institute, Research Scholar
443.225.9185
Related
Ontology requests: #11375
GO should have specific classes for the the walls of bacterial and protist cysts, especially if these are non-homologous and composed of different structures. We always get into trouble when we force annotation to a generic grouping class.
We also need this since cyst walls for taxon X are not fully classified
is_a GO:0005618 ! cell wall is_a GO:0009274 ! peptidoglycan-based cell wall <-- bacterial cell wall here? is_a GO:0009277 ! fungal-type cell wall <-- is this a type of chitin cell wall? like a protozoan cell wall? If so add a composition based grouping is_a GO:0009505 ! plant-type cell wall is_a GO:0031160 ! spore wall is_a GO:0097570 ! cyst wall ***