Re: [sbml-discuss] 有人请求加入“sbml-discuss”群组
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Michael Hucka
Mar 2, 2021, 11:31:04 PM3/2/21
to sbml-d...@googlegroups.com, howitwo...@gmail.com
Hi,
It's a good question. Basically, identifiers and names in a model can
be arbitrary -- they cannot be assumed to be interpretable. Sometimes,
some people and some software do use meaningful id's or names, but it is
a convention adopted by the authors. You would have to know the
conventions used by a given author or software tool, and there is no
guarantee that any other author or tool will follow the same convention
for id's and names.
The best way to identify and describe species and compartments is to use
what is called "annotations". These are structured (XML) and there are
agreed-upon conventions for using annotations to refer to well-known
databases and vocabularies. By annotating a given species or
compartment in a model with references to vocabularies and other
sources, it is possible to communicate more precisely the identity, or
meaning, or other aspects of that species or compartment. Similarly, by
reading annotations, a software tool can determine the identities and
meanings, and use this information when comparing species and
compartments between different annotated models.
I hope this helps!
Best regards,
MH
On 1 Mar 2021, at 1:31, sbml-discuss wrote:
> 来自 howitwo...@gmail.com 的消息：
> working on a tool that can merge the models in SBML files (in
> biomodels)to reconsturct a network. wonderring how to compare the
> different species and compartments. i use the name and id , but i
> wondering if there is some same elements(species and compartments)
> with different names. Them, i use id , but there may have ids in
> different database.
> this question wonders me a lot , i would be very apperciate if
> someone can answer me.
>
It's a good question. Basically, identifiers and names in a model can
be arbitrary -- they cannot be assumed to be interpretable. Sometimes,
some people and some software do use meaningful id's or names, but it is
a convention adopted by the authors. You would have to know the
conventions used by a given author or software tool, and there is no
guarantee that any other author or tool will follow the same convention
for id's and names.
The best way to identify and describe species and compartments is to use
what is called "annotations". These are structured (XML) and there are
agreed-upon conventions for using annotations to refer to well-known
databases and vocabularies. By annotating a given species or
compartment in a model with references to vocabularies and other
sources, it is possible to communicate more precisely the identity, or
meaning, or other aspects of that species or compartment. Similarly, by
reading annotations, a software tool can determine the identities and
meanings, and use this information when comparing species and
compartments between different annotated models.
I hope this helps!
Best regards,
MH
On 1 Mar 2021, at 1:31, sbml-discuss wrote:
> 来自 howitwo...@gmail.com 的消息：
> working on a tool that can merge the models in SBML files (in
> biomodels)to reconsturct a network. wonderring how to compare the
> different species and compartments. i use the name and id , but i
> wondering if there is some same elements(species and compartments)
> with different names. Them, i use id , but there may have ids in
> different database.
> this question wonders me a lot , i would be very apperciate if
> someone can answer me.
>
cruse hu
Mar 3, 2021, 12:12:30 AM3/3/21
to Michael Hucka, sbml-d...@googlegroups.com
Mendes,Pedro
Mar 3, 2021, 7:33:51 AM3/3/21
to sbml-d...@googlegroups.com
A good discussion about this can be found in the paper below, where the main difficulty of that exercise was really figuring out what is what (ie the problem of naming and uniquely identifying entities)
Herrgard et al (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnol. 26(10): 1155–1160.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018421/
Herrgard et al (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnol. 26(10): 1155–1160.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018421/
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