Change name to OGG from GGO. RE: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
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He, Yongqun
Oct 29, 2013, 7:46:42 PM10/29/13
to obo-d...@lists.sourceforge.net, Lindsay Cowell, Ramona Walls, ggo-d...@googlegroups.com, Cathy Wu, Liu, Yue, ogg-d...@googlegroups.com, Darren Natale (dan5@georgetown.edu)
Dr. Barry Smith kindly commented to me that the GGO (Genome and Gene Ontology) is not well named since it might suggest a confused relation to the Gene Ontology (GO). I agreed with the comment and proposed a new name "Ontology of Genes and Genomes (OGG)". Barry agreed. Asiyah also thought that it would be a good change. I have also communicated with PRO. Darren commented that with the new OGG ontology, "there is no clash with PRO". These are all good news. I look forward to close collaboration with BFO, PRO, and the OBO foundry community. Thanks!
Therefore, we will change GGO to the new name OGG or "Ontology of Genes and Genomes" from now on.
Corresponding to this name change, I have done a few things:
(1) Generated a new OGG OWL version. Current OGG is the same as previous GGO except that all "GGO_" and "ggo.owl" have been changed to "OGG_" and "ogg.owl".
(2) Generated a new OGG Google code project:
https://code.google.com/p/ogg/
I have also committed the new OGG OWL file and svn hierarchy to the Google code project.
(3) Generated a new ogg-discuss Google Group:
https://groups.google.com/forum/#!forum/ogg-discuss
It is open to the public for registration and posting. I feel very sorry that many have already registered for the ggo-discuss group, and now need to change to ogg-discuss. Thanks for your support!
Anyone is welcome to register and post in this Google Group. We may soon not post many emails to the obo-discuss mailing list, and instead primarily use the ogg-d...@googlegroups.com email address for discussion. If you have consistent interest in OGG development and applications and want to receive related emails and involve more discussions, please register an account in ogg-discuss. Thank you!
(4) Loaded the OGG to the Ontobee. Here is the Ontobee site for OGG:
http://www.ontobee.org/browser/index.php?o=OGG
With this new site available now in Ontobee, I have removed GGO from Ontobee.
My strong feeling is that the enthusiasm for OGG is very high. We will keep working on it and keep you updated. Thanks, all!
Oliver He
University of Michigan Medical School
-----Original Message-----
From: He, Yongqun [mailto:yong...@med.umich.edu]
Sent: Tuesday, October 29, 2013 10:34 AM
To: Lindsay Cowell; <obo-d...@lists.sourceforge.net>
Cc: Ramona Walls; ggo-d...@googlegroups.com; Cathy Wu; obo-d...@lists.sourceforge.net; Liu, Yue
Subject: Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
I agree with Lindsay that we don’t want to introduce new ontology terms for gene and genome. We only generate new ontology terms when there are no such terms, or the meanings are different.
As far as I know, there are not specific ontology gene terms like 'gene of homo sapiens' (or 'human gene', 'gene of Escherichia coli' (or 'E. coli g ene'), ‘gene of Escherichia coli str. K-12 substr. MG1655‘, and more specific genes such as genes for human p53, E. coli sod1, etc. These terms are the first time proposed and have not been generated in ontologies (at least in an OBO foundry ontology) as I recognize. Therefore, we generate new terms for them and develop a strategy to represent them systematically.
However, we do have possible issue with the two terms 'gene' and 'genome' per se, because these two terms have been defined in SO. We don't mean to duplicate the two terms. We just don't know if our GGO terms have the same meanings as the two SO terms. Below is some explanation:
For the GGO term 'gene' (GGO_0000000002), here is our definition:
"a gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule."
This definition comes from the NCBI-recommended book "Molecular Cell Biology. 4th edition":
http://www.ncbi.nlm.nih.gov/books/NBK21640/
Here is a paragraph of text quoted from the above book and website:
" In molecular terms, a gene commonly is defined as the entire nucleic acid sequence that is necessary for the synthesis of a functional polypeptide. According to this definition, a gene includes more than the nucleotides encoding the amino acid sequence of a protein, referred to as the coding region. A gene also includes all the DNA sequences required for synthesis of a particular RNA transcript. In some prokaryotic genes, DNA sequences controlling the initiation of transcription by RNA polymerase can lie thousands of base pairs from the coding region. In eukaryotic genes, transcription-control regions known as enhancers can lie 50 kb or more from the coding region. Other critical noncoding regions in eukaryotic genes are the sequences that specify 3′ cleavage and polyadenylation [poly(A) sites] and splicing of primary RNA transcripts. Mutations in these RNAprocessing signals prevent expression of a functional mRNA and thus of the encoded polypeptide."
I totally agree with the definition of the term 'gene' in here.
One key factor in my mind is that GGO defines 'gene' as a material entity, but I don't know if the SO 'gene' definition agrees with it. In SO, the term 'gene' (http://purl.obolibrary.org/obo/SO_0000704) is defined as:
"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. "
Its root term is: sequence_feature (SO_0000110), which is defined as:
"An extent of biological sequence."
Here, I don't know if the "biological sequence" in SO is also a material entity, or a "sequence information" that may be classified as an IAO 'information content entity' (ICE).
As I view it, a gene material entity can be documented by its gene sequence information. The gene sequence information is an IAO 'information content entity'. I think we will need some term like 'gene sequence information' or something similar. I don't know if the SO:sequence fits in this category.
Similar comparison applies to the GGO:genome and SO:genome.
Darren: I am glad that you think GGO "could not be more timely". To address your question about cross-reference in different database, a simple answer is: Yes.
To do the cross reference task, currently GGO use the oboInOWL annotation property called "database_cross_reference".
For example, for the human p53 gene (GGO_3000007157. Here is the Ontobee link:
http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibrary.org/obo/GGO_3000007157 ), we have the following annotation statement:
"database_cross_reference: MIM:191170, HPRD:01859, Vega:OTTHUMG00000162125, HGNC:11998, Ensembl:ENSG00000141510"
So as you see, here we include the HGNC for human. And we include more databases including Ensembl, MIM, and HPRD. For a mouse gene, we will include MGI.
Beside the annotation assignment, I also plan to define some logical axiom like this:
'human gene p53':
'cross-reference database' value 'HGNC' and ('has database id' value 11998) A general design pattern would be:
(A gene) 'cross-reference database' value (a database) and ('has database id' value string)
In this design pattern, I propose two object property relations 'cross-reference database' and 'has database id'. The term 'HGNC' is an instance of some class term called 'database' (or called something similar). The value '11998' is an integer or string. The use of the object property relation-based axiom may support better SPARQL query (at least for some users). We can have both the annotation version and the object property definition version co-exist.
I guess that we will need to talk about how to link GGO with PRO. I think some relation like 'encodes for' can be used. The design pattern can be:
a 'gene' 'encodes for' some 'protein'.
Thanks!
Oliver
-----Original Message-----
From: Lindsay Cowell [mailto:Lindsay...@UTSouthwestern.edu]
Sent: Monday, October 28, 2013 10:24 PM
To: <obo-d...@lists.sourceforge.net>
Cc: He, Yongqun; Ramona Walls; ggo-d...@googlegroups.com; Liu, Yue; obo-d...@lists.sourceforge.net; Cathy Wu
Subject: Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
I highly recommend that we do not introduce new terms for gene and genome.
Sent from my iPad
On Oct 28, 2013, at 8:11 PM, "Darren Natale" <da...@georgetown.edu> wrote:
> Apologies for cross-posting.
>
> This could not be more timely. In the last few releases, PRO has made
> connections between our protein terms and the genes that encode them.
> We have thus far used the model organism databases as the references.
> So, HGNC for human, MGI for mouse, etc, and only use the secondary
> database Entrez Gene whenever no entry exists in a model organism
> database for the required gene. Will GGO cross-reference these (and others)?
>
> Also, a note of caution about the 'gene' term. While I agree that a
> gene is not really a sequence feature (unless that term is defined as
> being part of some material entity), I have yet to see a gene exist as
> an entity unto itself. How do you define gene in GGO?
>
> On 10/28/2013 5:56 PM, He, Yongqun wrote:
>> Here are some communications following my yesterday’s GGO
>> announcement …
>>
>> I now post this to the obo-discuss mailing list. I also post it to
>> the newly generated ggo-discuss mailing list by following Chris’ suggestion.
>> The ggo-discuss Google mailing list is here:
>>
>> https://groups.google.com/forum/#!forum/ggo-discuss
>>
>> this mailing list is set up to be open to everyone!
>>
>> Any suggestion and comments are welcome. Thanks!
>>
>> Oliver
>>
>> *From:*bfo-d...@googlegroups.com
>> [mailto:bfo-d...@googlegroups.com] *On Behalf Of *He, Yongqun
>> *Sent:* Monday, October 28, 2013 5:07 PM
>> *To:* Ramona Walls
>> *Cc:* OBI Developers (obi-...@lists.sourceforge.net);
>> bfo-d...@googlegroups.com; da...@georgetown.edu; Cathy Wu; Liu, Yue
>> *Subject:* [bfo-discuss] RE: [Obi-devel] Announce a Genome and Gene
>> Ontology (GGO)
>>
>> Dear Ramona,
>>
>> Thank you for your positive comment. Here are my answers to your good
>> questions:
>>
>> --
>>
>> GGO vs SO:
>>
>> The GGO focuses on representing individual reference genomes and
>> genes of biological organisms. Currently it does not include any
>> sequence information for any gene or genome yet. The reason we have
>> done this way is that the size of gene sequences for all the genes
>> can be huge. We will need to do some testing first. Anyway, with the
>> GeneID available, the gene sequence can be extracted automatically
>> from NCBI or other resources.
>>
>> For sure we would like to add links and align GGO with SO. I will
>> look into it in more detail later. Note that SO also includes the
>> terms “genome” and “gene”. I am not sure if these two SO terms have
>> the same meanings as the corresponding GGO terms. The root of
>> SO:genome is ‘SO:sequence collection’, and the root of SO:gene is
>> ‘SO:sequence feature’. I am not sure how SO roots are aligned with
>> BFO. Our GGO “genome” and “gene” are under ‘BFO:material entity’. I
>> think that the gene material may be different from the gene sequence information itself.
>>
>> --
>>
>> About new GGO IDs:
>>
>> A note is that GGO IDs map to NCBI Entrez Gene IDs, which are
>> different from GenBank IDs. As I recall, the Entrez GeneIDs come from
>> RefSeq, which is a database of NCBI manually curated reference data.
>> The GenBank includes customer-submitted data which may not be
>> manually and carefully checked by the NCBI team.
>>
>> Rationale about the GGO IDs design:
>>
>> First, yes, the NCBI gene database includes gene ID, and for each
>> gene ID, there is a URI. For example, for p53, the URI is:
>> http://www.ncbi.nlm.nih.gov/gene/7157. However, the URI does not
>> point to an ontology term. The NCBI Entrez Gene system is not an ontology.
>>
>> Second, we cannot directly use the NCBI GeneID. Our first GGO ID:
>> GGO_0000000001 is reserved for “genome”, and our second is for “gene”.
>> However, NCBI GeneIDs of 1 and 2 mean some specific genes, which are
>> quite different:
>>
>> http://www.ncbi.nlm.nih.gov/gene/1
>>
>> http://www.ncbi.nlm.nih.gov/gene/2
>>
>> Similarly, many other NCBI GeneIDs such as 4, 5, …. are quite
>> different from our GGO IDs of 4 (GGO_0000000004), 5 (GGO_0000000005), etc.
>> Therefore, we will need to use some different GGO IDs instead of
>> directly using the GeneIDs.
>>
>> Third, one possible question is here: why bother to do the mapping at
>> all and why not use totally new random GGO IDs for every GGO gene
>> ontology term? Well, we considered this option, and this is my idea
>> to better do the mapping instead of generating random IDs. My reason
>> is that there are too many genes in the world. A single GGO that
>> covers all possible genes may be hard to maintain and use. If we
>> separate GGO into different subsets based on organism taxid or other
>> criteria, the randomly given GGO Ids may be hard to coordinate
>> between different subsets. By mapping the GGO IDs to GeneIDs and
>> NCBITaxon IDs, we have basically generated a naming strategy that
>> predefines all the specific genes available in Entrez Gene database
>> available, and all the genomes as well. With this strategy, we don’t
>> need to worry that much about GGO IDs for genes and genomes.
>>
>> Fourth, beside specific genes, GGO also includes genomes. In NCBI
>> Genome database, each genome also has an ID. However, GGO does not
>> decide to use the genome ID because we think there is a better
>> option: mapping the GGO ID of a ‘genome of taxon_label_X’ to the
>> taxon ID (as I described in my previous email). It’s more meaningful
>> and easy to do. We don’t know if a NCBI Genome ID may change or not.
>> However, we are more sure that NCBITaxon is likely very stable since it is an ontology now.
>>
>> In addition, GGO has terms like “gene of organism”, for example,
>> ‘gene of homo sapiens’, ‘gene or E. coli’, ‘gene of Escherichia coli
>> str. K-12 substr. MG1655‘. We also designed the GGO ID naming
>> strategy for these terms. I believe that we have chosen a workable
>> and easy-to-use strategy. GGO has includes the hierarchical structure
>> of different gene types, such as the is_a relation between ‘gene or
>> E. coli’ and ‘gene of Escherichia coli str. K-12 substr. MG1655‘.
>>
>> The NCBI group has developed many wonderful biological systems
>> including the NCBI Taxonomy, Entrez Gene, and NCBI Genome projects.
>> The development of GGO is targeted to reuse these NCBI resources for
>> the ontology developers and users, including ourselves. We also plan
>> to link more information from NCBI or other resources to GGO, such as
>> linking genes to corresponding Gene Ontology (GO) IDs, PubMed IDs,
>> interaction database IDs, VO vaccine IDs, etc. I would also like to
>> contact the NCBI group soon and discuss some possible collaboration if they are interested!
>>
>> GGO is developed by following the OBO foundry principles including
>> openness and collaboration. GGO is developed to address a critical
>> need in the biological ontology community. We look forward to further
>> collaborating with everyone who is interested. Thanks!
>>
>> Best,
>>
>> Oliver
>>
>> *From:*rlwal...@gmail.com <mailto:rlwal...@gmail.com>
>> [mailto:rlwal...@gmail.com] *On Behalf Of *Ramona Walls
>> *Sent:* Monday, October 28, 2013 2:50 PM
>> *To:* He, Yongqun
>> *Cc:* OBI Developers (obi-...@lists.sourceforge.net
>> <mailto:obi-...@lists.sourceforge.net>);
>> bfo-d...@googlegroups.com <mailto:bfo-d...@googlegroups.com>;
>> vaccineont...@lists.sourceforge.net
>> <mailto:vaccineont...@lists.sourceforge.net>;
>> da...@georgetown.edu <mailto:da...@georgetown.edu>; Cathy Wu; Liu, Yue
>> *Subject:* Re: [Obi-devel] Announce a Genome and Gene Ontology (GGO)
>>
>> Dear Oliver,
>>
>> GGO sounds like a very useful ontology. I have just a few questions:
>>
>> Could you explain the relationships between GGO and SO (if any) and
>> if you plan to add links (relations) between them?
>>
>> Could you provide you rationale behind creating new IDs for all of
>> the genes in Genbank, rather than using the genbank IDs? I understand
>> that the ability to resolve in Ontobee is important, but I am worried
>> about the duplication of IDs. Does Genbank have URIs for its gene
>> IDs? If so, does it make sense to add an OWL same as relation between
>> the GGO urls and the Genbank urls?
>>
>> Ramona
>>
>>
>> ------------------------------------------------------
>> Ramona L. Walls, Ph.D.
>> Scientific Analyst
>> The iPlant Collaborative
>> Thomas J. Keating Bioresearch Building
>>
>> 1657 East Helen St
>>
>> Tucson, AZ 85721
>> tel: 520.626.1489
>> fax: 520.626.4824
>> rwa...@iplantcollaborative.org
>> <mailto:rwa...@iplantcollaborative.org>
>>
>> On Sun, Oct 27, 2013 at 4:00 PM, He, Yongqun <yong...@med.umich.edu
>> <mailto:yong...@med.umich.edu>> wrote:
>>
>> Dear friends,
>>
>> Here I want to announce a new ontology called GGO: Genome and Gene
>> Ontology, developed by Yue Liu and me from the University of Michigan.
>> Here I want to introduce some basic information about GGO.
>>
>> As we know, the Gene Ontology (GO) is really not about gene, it’s
>> about biological processes, molecular functions, and cellular components.
>> There is no ontology that represents individual reference genes of
>> different genomes. *As I believe, the lack of such an ontology for
>> individual genes has become a major bottleneck in the biological
>> ontology community.* The purpose of the GGO development is to address
>> this critical need. GGO aims to represent millions of reference genes
>> of different genomes of different species available in the NCBI Gene
>> database. As a demonstration, the current GGO version represents the
>> genomes and genes of human and a representative E. coli genome.
>>
>> Here is the GGO Ontobee website:
>>
>> http://www.ontobee.org/browser/index.php?o=GGO
>>
>> Here is the GGO Google code website:
>>
>> https://code.google.com/p/ggo/
>>
>> Some basic description of our GGO development strategy:
>>
>> -*Top level alignment*: GGO aligns with the Basic Formal Ontology 2
>> (BFO
>> 2) top ontology. GGO also aligns with other OBO Foundry ontologies,
>> including the NCBITaxon, OBI, and IAO.
>>
>> -*GGO Genome term design*: Use NCBITaxon to represent organism
>> taxonomy terms and hierarchy. The GGO genome term IRIs are generated
>> by mapping the IDs to the NCBITaxon term IRIs. With this design, the
>> GGO genome term IRIs are predefined based on NCBITaxon records.
>>
>> -*GGO Gene term design*: Extract the information from the NCBI Gene
>> Database and use the information to represent gene information. The
>> mapping between NCBI GeneID and GGO gene IDs will be made, so that
>> GGO gene term IRIs are predefined based on NCBI GeneIDs.
>>
>> -Here is the statistics of current GGO:
>> http://www.ontobee.org/ontostat.php?ontology=GGO
>>
>> Here is some specific explanation:
>>
>> *GGO term prefix*: GGO term IRIs are generated usign the prefix "GGO_"
>> followed by 10 digital numbers.
>>
>> Two key terms:
>>
>> -GGO 'genome': GGO ID: GGO_0000000001
>>
>> -GGO 'gene': GGO ID: GGO_0000000002
>>
>> *Specific GGO genome term*: For each GGO genome term, use the
>> following
>> pattern:
>>
>> * *Label*: "genome of [NCBITaxon lable]"
>> * *GGO ID*: "GGO_{1000000000 + taxon ID}"
>> * *Hierarchy*: follow the same hierarchy as shown in NCBITaxon
>> * *Example*: for human (homo sapiens; NCBITaxon_NCBITaxon_9606):
>>
>> o GGO genome term label: 'genome of Homo sapiens'
>> o GGO IRI: "GGO_{1000000000 + 9606}" = 'GGO_1000009606'
>>
>> *For general GGO gene term*: For each GGO gene term, use the
>> following
>> pattern:
>>
>> * *Label*: "gene of [NCBITaxon lable]"
>> * *GGO ID*: "GGO_{2000000000 + taxon ID}"
>> * *Hierarchy*: follow the same hierarchy as shown in NCBITaxon
>> * *Example*: for human (homo sapiens; NCBITaxon_NCBITaxon_9606):
>>
>> o GGO genome gene term label: 'gene of Homo sapiens'
>> o GGO IRI: "GGO_{2000000000 + 9606}" = 'GGO_2000009606'
>>
>> *For specific GGO gene term: *For each specific GGO gene term, use
>> the following pattern:
>>
>> * *Label*: add the gene symbol as provided by NCBI Gene database.
>> * *GGO ID*: "GGO_{3000000000 + NCBI GeneID}"
>> * *Hierarchy*: position under the "gene of NCBITaxon label" as shown
>> above.
>> * *Example*: for human gene TP53 p53 that has GeneID of 7157
>> <http://www.ncbi.nlm.nih.gov/gene/7157>:
>>
>> o GGO specific gene term label: 'TP53' (the official gene symbol)
>> o GGO gene term synonyms: use the synonyms provided by the
>> NCBI Gene database.
>> o GGO IRI: "GGO_{3000000000 + 7157}" = 'GGO_3000007157'
>> o See:
>>
>> http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibra
>> ry.org/obo/GGO_3000007157
>>
>> <http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibr
>> ary.org/obo/GGO_3000007157>
>>
>> o Check an E. coli example:
>>
>> http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibra
>> ry.org/obo/GGO_3000006647
>>
>> <http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibr
>> ary.org/obo/GGO_3000006647>
>>
>>
>> As seen on the above two samples, for each specific gene, GGO has
>> included many attributes retrieved from the NCBI Gene database, such
>> as gene symbol and synonyms, GeneID, locus tag and other database
>> cross reference IDs, gene annotation, gene type, … We plan to add
>> more information later.
>>
>> Note that with the above design, we have predefined about one million
>> of GGO genome IDs (since NCBOTaxon has about 1 mill terms), and over
>> 10 million of GGO gene IDs (since over 10 mill NCBI Gene IDs exist).
>> I am happy to provide more information later about the GGO rationale
>> and development strategy.
>>
>> As an aside: with the GGO support, we can now query Ontobee for human
>> or E. coli genes, such as:
>>
>> Search human genes containing “TP53”:
>>
>> http://www.ontobee.org/browser/index.php?keywords=TP53&Submit2=Search
>> +terms&o=GGO
>> <http://www.ontobee.org/browser/index.php?keywords=TP53&Submit2=Searc
>> h+terms&o=GGO>
>>
>>
>> Search human genes containing “sod1”:
>>
>> http://www.ontobee.org/browser/index.php?keywords=sod1&Submit2=Search
>> +terms&o=GGO
>> <http://www.ontobee.org/browser/index.php?keywords=sod1&Submit2=Searc
>> h+terms&o=GGO>
>>
>> In addition, we have developed a software program to automatically
>> generate GGO subset ontology for each genome based on NCBITaxon ID.
>> We will post the results for different genomes of commonly studied
>> organisms in a website soon.
>>
>> Our program to generate a GGO subset for various genes from different
>> genomes is about ready. Our use case is to generate GGO terms and
>> hierarchy for many gene terms from different eukaryotic, prokaryotic,
>> and viral organisms that are curated and collected in the Vaccine
>> Ontology (VO). Currently, those genes collected in VO use VO prefix
>> IDs, which is obviously not optimal. The VO use case is also a
>> motivation for our GGO development. I think different people may have
>> different use cases as well.
>>
>> Relation to other ontologies:
>>
>> -GGO is not like any other existing ontology. GGO is a new ontology
>> that integrates existing non-ontology data particularly the NCBI Gene
>> database data.
>>
>> -GGO vs PRO: GGO represents genomes and genes where a genome includes
>> many genes. GGO is not meant to represent proteins. Proteins are the
>> products of genes and are represented in the Protein Ontology (PRO).
>> Proteins are more complex than genes, at least in eukaryotic systems.
>> Each gene may encode for different proteins, esp. in eukaryotic
>> organisms. We look forward to collaborating with PRO and other
>> ontologies to explore how GGO can link and help ontological protein
>> representation.
>>
>> I believe that GGO will have some great values. GGO will for sure be
>> further developed in different directions. We are happy to discuss
>> with anyone who is interested.
>>
>> Any suggestions and feedback are welcome. Thank you!
>>
>> Oliver
>>
>> Yongqun "Oliver" He, DVM, PhD
>>
>> Associate Professor
>>
>> Unit for Laboratory Animal Medicine
>>
>> Department of Microbiology and Immunology
>>
>> Center for Computational Medicine and Bioinformatics
>>
>> and Comprehensive Cancer Center
>>
>> University of Michigan Medical School
>>
>> Mail: 018 ARF, 1150 W. Medical Center Dr.
>>
>> Ann Arbor, MI 48109
>>
>> Email: yong...@med.umich.edu <mailto:yong...@med.umich.edu>
>>
>> Tel: 734-615-8231 <tel:734-615-8231> (O)
>>
>> http://www.hegroup.org/
>>
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Therefore, we will change GGO to the new name OGG or "Ontology of Genes and Genomes" from now on.
Corresponding to this name change, I have done a few things:
(1) Generated a new OGG OWL version. Current OGG is the same as previous GGO except that all "GGO_" and "ggo.owl" have been changed to "OGG_" and "ogg.owl".
(2) Generated a new OGG Google code project:
https://code.google.com/p/ogg/
I have also committed the new OGG OWL file and svn hierarchy to the Google code project.
(3) Generated a new ogg-discuss Google Group:
https://groups.google.com/forum/#!forum/ogg-discuss
It is open to the public for registration and posting. I feel very sorry that many have already registered for the ggo-discuss group, and now need to change to ogg-discuss. Thanks for your support!
Anyone is welcome to register and post in this Google Group. We may soon not post many emails to the obo-discuss mailing list, and instead primarily use the ogg-d...@googlegroups.com email address for discussion. If you have consistent interest in OGG development and applications and want to receive related emails and involve more discussions, please register an account in ogg-discuss. Thank you!
(4) Loaded the OGG to the Ontobee. Here is the Ontobee site for OGG:
http://www.ontobee.org/browser/index.php?o=OGG
With this new site available now in Ontobee, I have removed GGO from Ontobee.
My strong feeling is that the enthusiasm for OGG is very high. We will keep working on it and keep you updated. Thanks, all!
Oliver He
University of Michigan Medical School
-----Original Message-----
From: He, Yongqun [mailto:yong...@med.umich.edu]
Sent: Tuesday, October 29, 2013 10:34 AM
To: Lindsay Cowell; <obo-d...@lists.sourceforge.net>
Cc: Ramona Walls; ggo-d...@googlegroups.com; Cathy Wu; obo-d...@lists.sourceforge.net; Liu, Yue
Subject: Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
I agree with Lindsay that we don’t want to introduce new ontology terms for gene and genome. We only generate new ontology terms when there are no such terms, or the meanings are different.
As far as I know, there are not specific ontology gene terms like 'gene of homo sapiens' (or 'human gene', 'gene of Escherichia coli' (or 'E. coli g ene'), ‘gene of Escherichia coli str. K-12 substr. MG1655‘, and more specific genes such as genes for human p53, E. coli sod1, etc. These terms are the first time proposed and have not been generated in ontologies (at least in an OBO foundry ontology) as I recognize. Therefore, we generate new terms for them and develop a strategy to represent them systematically.
However, we do have possible issue with the two terms 'gene' and 'genome' per se, because these two terms have been defined in SO. We don't mean to duplicate the two terms. We just don't know if our GGO terms have the same meanings as the two SO terms. Below is some explanation:
For the GGO term 'gene' (GGO_0000000002), here is our definition:
"a gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule."
This definition comes from the NCBI-recommended book "Molecular Cell Biology. 4th edition":
http://www.ncbi.nlm.nih.gov/books/NBK21640/
Here is a paragraph of text quoted from the above book and website:
" In molecular terms, a gene commonly is defined as the entire nucleic acid sequence that is necessary for the synthesis of a functional polypeptide. According to this definition, a gene includes more than the nucleotides encoding the amino acid sequence of a protein, referred to as the coding region. A gene also includes all the DNA sequences required for synthesis of a particular RNA transcript. In some prokaryotic genes, DNA sequences controlling the initiation of transcription by RNA polymerase can lie thousands of base pairs from the coding region. In eukaryotic genes, transcription-control regions known as enhancers can lie 50 kb or more from the coding region. Other critical noncoding regions in eukaryotic genes are the sequences that specify 3′ cleavage and polyadenylation [poly(A) sites] and splicing of primary RNA transcripts. Mutations in these RNAprocessing signals prevent expression of a functional mRNA and thus of the encoded polypeptide."
I totally agree with the definition of the term 'gene' in here.
One key factor in my mind is that GGO defines 'gene' as a material entity, but I don't know if the SO 'gene' definition agrees with it. In SO, the term 'gene' (http://purl.obolibrary.org/obo/SO_0000704) is defined as:
"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. "
Its root term is: sequence_feature (SO_0000110), which is defined as:
"An extent of biological sequence."
Here, I don't know if the "biological sequence" in SO is also a material entity, or a "sequence information" that may be classified as an IAO 'information content entity' (ICE).
As I view it, a gene material entity can be documented by its gene sequence information. The gene sequence information is an IAO 'information content entity'. I think we will need some term like 'gene sequence information' or something similar. I don't know if the SO:sequence fits in this category.
Similar comparison applies to the GGO:genome and SO:genome.
Darren: I am glad that you think GGO "could not be more timely". To address your question about cross-reference in different database, a simple answer is: Yes.
To do the cross reference task, currently GGO use the oboInOWL annotation property called "database_cross_reference".
For example, for the human p53 gene (GGO_3000007157. Here is the Ontobee link:
http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibrary.org/obo/GGO_3000007157 ), we have the following annotation statement:
"database_cross_reference: MIM:191170, HPRD:01859, Vega:OTTHUMG00000162125, HGNC:11998, Ensembl:ENSG00000141510"
So as you see, here we include the HGNC for human. And we include more databases including Ensembl, MIM, and HPRD. For a mouse gene, we will include MGI.
Beside the annotation assignment, I also plan to define some logical axiom like this:
'human gene p53':
'cross-reference database' value 'HGNC' and ('has database id' value 11998) A general design pattern would be:
(A gene) 'cross-reference database' value (a database) and ('has database id' value string)
In this design pattern, I propose two object property relations 'cross-reference database' and 'has database id'. The term 'HGNC' is an instance of some class term called 'database' (or called something similar). The value '11998' is an integer or string. The use of the object property relation-based axiom may support better SPARQL query (at least for some users). We can have both the annotation version and the object property definition version co-exist.
I guess that we will need to talk about how to link GGO with PRO. I think some relation like 'encodes for' can be used. The design pattern can be:
a 'gene' 'encodes for' some 'protein'.
Thanks!
Oliver
-----Original Message-----
From: Lindsay Cowell [mailto:Lindsay...@UTSouthwestern.edu]
Sent: Monday, October 28, 2013 10:24 PM
To: <obo-d...@lists.sourceforge.net>
Cc: He, Yongqun; Ramona Walls; ggo-d...@googlegroups.com; Liu, Yue; obo-d...@lists.sourceforge.net; Cathy Wu
Subject: Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
I highly recommend that we do not introduce new terms for gene and genome.
Sent from my iPad
On Oct 28, 2013, at 8:11 PM, "Darren Natale" <da...@georgetown.edu> wrote:
> Apologies for cross-posting.
>
> This could not be more timely. In the last few releases, PRO has made
> connections between our protein terms and the genes that encode them.
> We have thus far used the model organism databases as the references.
> So, HGNC for human, MGI for mouse, etc, and only use the secondary
> database Entrez Gene whenever no entry exists in a model organism
> database for the required gene. Will GGO cross-reference these (and others)?
>
> Also, a note of caution about the 'gene' term. While I agree that a
> gene is not really a sequence feature (unless that term is defined as
> being part of some material entity), I have yet to see a gene exist as
> an entity unto itself. How do you define gene in GGO?
>
> On 10/28/2013 5:56 PM, He, Yongqun wrote:
>> Here are some communications following my yesterday’s GGO
>> announcement …
>>
>> I now post this to the obo-discuss mailing list. I also post it to
>> the newly generated ggo-discuss mailing list by following Chris’ suggestion.
>> The ggo-discuss Google mailing list is here:
>>
>> https://groups.google.com/forum/#!forum/ggo-discuss
>>
>> this mailing list is set up to be open to everyone!
>>
>> Any suggestion and comments are welcome. Thanks!
>>
>> Oliver
>>
>> *From:*bfo-d...@googlegroups.com
>> [mailto:bfo-d...@googlegroups.com] *On Behalf Of *He, Yongqun
>> *Sent:* Monday, October 28, 2013 5:07 PM
>> *To:* Ramona Walls
>> *Cc:* OBI Developers (obi-...@lists.sourceforge.net);
>> bfo-d...@googlegroups.com; da...@georgetown.edu; Cathy Wu; Liu, Yue
>> *Subject:* [bfo-discuss] RE: [Obi-devel] Announce a Genome and Gene
>> Ontology (GGO)
>>
>> Dear Ramona,
>>
>> Thank you for your positive comment. Here are my answers to your good
>> questions:
>>
>> --
>>
>> GGO vs SO:
>>
>> The GGO focuses on representing individual reference genomes and
>> genes of biological organisms. Currently it does not include any
>> sequence information for any gene or genome yet. The reason we have
>> done this way is that the size of gene sequences for all the genes
>> can be huge. We will need to do some testing first. Anyway, with the
>> GeneID available, the gene sequence can be extracted automatically
>> from NCBI or other resources.
>>
>> For sure we would like to add links and align GGO with SO. I will
>> look into it in more detail later. Note that SO also includes the
>> terms “genome” and “gene”. I am not sure if these two SO terms have
>> the same meanings as the corresponding GGO terms. The root of
>> SO:genome is ‘SO:sequence collection’, and the root of SO:gene is
>> ‘SO:sequence feature’. I am not sure how SO roots are aligned with
>> BFO. Our GGO “genome” and “gene” are under ‘BFO:material entity’. I
>> think that the gene material may be different from the gene sequence information itself.
>>
>> --
>>
>> About new GGO IDs:
>>
>> A note is that GGO IDs map to NCBI Entrez Gene IDs, which are
>> different from GenBank IDs. As I recall, the Entrez GeneIDs come from
>> RefSeq, which is a database of NCBI manually curated reference data.
>> The GenBank includes customer-submitted data which may not be
>> manually and carefully checked by the NCBI team.
>>
>> Rationale about the GGO IDs design:
>>
>> First, yes, the NCBI gene database includes gene ID, and for each
>> gene ID, there is a URI. For example, for p53, the URI is:
>> http://www.ncbi.nlm.nih.gov/gene/7157. However, the URI does not
>> point to an ontology term. The NCBI Entrez Gene system is not an ontology.
>>
>> Second, we cannot directly use the NCBI GeneID. Our first GGO ID:
>> GGO_0000000001 is reserved for “genome”, and our second is for “gene”.
>> However, NCBI GeneIDs of 1 and 2 mean some specific genes, which are
>> quite different:
>>
>> http://www.ncbi.nlm.nih.gov/gene/1
>>
>> http://www.ncbi.nlm.nih.gov/gene/2
>>
>> Similarly, many other NCBI GeneIDs such as 4, 5, …. are quite
>> different from our GGO IDs of 4 (GGO_0000000004), 5 (GGO_0000000005), etc.
>> Therefore, we will need to use some different GGO IDs instead of
>> directly using the GeneIDs.
>>
>> Third, one possible question is here: why bother to do the mapping at
>> all and why not use totally new random GGO IDs for every GGO gene
>> ontology term? Well, we considered this option, and this is my idea
>> to better do the mapping instead of generating random IDs. My reason
>> is that there are too many genes in the world. A single GGO that
>> covers all possible genes may be hard to maintain and use. If we
>> separate GGO into different subsets based on organism taxid or other
>> criteria, the randomly given GGO Ids may be hard to coordinate
>> between different subsets. By mapping the GGO IDs to GeneIDs and
>> NCBITaxon IDs, we have basically generated a naming strategy that
>> predefines all the specific genes available in Entrez Gene database
>> available, and all the genomes as well. With this strategy, we don’t
>> need to worry that much about GGO IDs for genes and genomes.
>>
>> Fourth, beside specific genes, GGO also includes genomes. In NCBI
>> Genome database, each genome also has an ID. However, GGO does not
>> decide to use the genome ID because we think there is a better
>> option: mapping the GGO ID of a ‘genome of taxon_label_X’ to the
>> taxon ID (as I described in my previous email). It’s more meaningful
>> and easy to do. We don’t know if a NCBI Genome ID may change or not.
>> However, we are more sure that NCBITaxon is likely very stable since it is an ontology now.
>>
>> In addition, GGO has terms like “gene of organism”, for example,
>> ‘gene of homo sapiens’, ‘gene or E. coli’, ‘gene of Escherichia coli
>> str. K-12 substr. MG1655‘. We also designed the GGO ID naming
>> strategy for these terms. I believe that we have chosen a workable
>> and easy-to-use strategy. GGO has includes the hierarchical structure
>> of different gene types, such as the is_a relation between ‘gene or
>> E. coli’ and ‘gene of Escherichia coli str. K-12 substr. MG1655‘.
>>
>> The NCBI group has developed many wonderful biological systems
>> including the NCBI Taxonomy, Entrez Gene, and NCBI Genome projects.
>> The development of GGO is targeted to reuse these NCBI resources for
>> the ontology developers and users, including ourselves. We also plan
>> to link more information from NCBI or other resources to GGO, such as
>> linking genes to corresponding Gene Ontology (GO) IDs, PubMed IDs,
>> interaction database IDs, VO vaccine IDs, etc. I would also like to
>> contact the NCBI group soon and discuss some possible collaboration if they are interested!
>>
>> GGO is developed by following the OBO foundry principles including
>> openness and collaboration. GGO is developed to address a critical
>> need in the biological ontology community. We look forward to further
>> collaborating with everyone who is interested. Thanks!
>>
>> Best,
>>
>> Oliver
>>
>> *From:*rlwal...@gmail.com <mailto:rlwal...@gmail.com>
>> [mailto:rlwal...@gmail.com] *On Behalf Of *Ramona Walls
>> *Sent:* Monday, October 28, 2013 2:50 PM
>> *To:* He, Yongqun
>> *Cc:* OBI Developers (obi-...@lists.sourceforge.net
>> <mailto:obi-...@lists.sourceforge.net>);
>> bfo-d...@googlegroups.com <mailto:bfo-d...@googlegroups.com>;
>> vaccineont...@lists.sourceforge.net
>> <mailto:vaccineont...@lists.sourceforge.net>;
>> da...@georgetown.edu <mailto:da...@georgetown.edu>; Cathy Wu; Liu, Yue
>> *Subject:* Re: [Obi-devel] Announce a Genome and Gene Ontology (GGO)
>>
>> Dear Oliver,
>>
>> GGO sounds like a very useful ontology. I have just a few questions:
>>
>> Could you explain the relationships between GGO and SO (if any) and
>> if you plan to add links (relations) between them?
>>
>> Could you provide you rationale behind creating new IDs for all of
>> the genes in Genbank, rather than using the genbank IDs? I understand
>> that the ability to resolve in Ontobee is important, but I am worried
>> about the duplication of IDs. Does Genbank have URIs for its gene
>> IDs? If so, does it make sense to add an OWL same as relation between
>> the GGO urls and the Genbank urls?
>>
>> Ramona
>>
>>
>> ------------------------------------------------------
>> Ramona L. Walls, Ph.D.
>> Scientific Analyst
>> The iPlant Collaborative
>> Thomas J. Keating Bioresearch Building
>>
>> 1657 East Helen St
>>
>> Tucson, AZ 85721
>> tel: 520.626.1489
>> fax: 520.626.4824
>> rwa...@iplantcollaborative.org
>> <mailto:rwa...@iplantcollaborative.org>
>>
>> On Sun, Oct 27, 2013 at 4:00 PM, He, Yongqun <yong...@med.umich.edu
>> <mailto:yong...@med.umich.edu>> wrote:
>>
>> Dear friends,
>>
>> Here I want to announce a new ontology called GGO: Genome and Gene
>> Ontology, developed by Yue Liu and me from the University of Michigan.
>> Here I want to introduce some basic information about GGO.
>>
>> As we know, the Gene Ontology (GO) is really not about gene, it’s
>> about biological processes, molecular functions, and cellular components.
>> There is no ontology that represents individual reference genes of
>> different genomes. *As I believe, the lack of such an ontology for
>> individual genes has become a major bottleneck in the biological
>> ontology community.* The purpose of the GGO development is to address
>> this critical need. GGO aims to represent millions of reference genes
>> of different genomes of different species available in the NCBI Gene
>> database. As a demonstration, the current GGO version represents the
>> genomes and genes of human and a representative E. coli genome.
>>
>> Here is the GGO Ontobee website:
>>
>> http://www.ontobee.org/browser/index.php?o=GGO
>>
>> Here is the GGO Google code website:
>>
>> https://code.google.com/p/ggo/
>>
>> Some basic description of our GGO development strategy:
>>
>> -*Top level alignment*: GGO aligns with the Basic Formal Ontology 2
>> (BFO
>> 2) top ontology. GGO also aligns with other OBO Foundry ontologies,
>> including the NCBITaxon, OBI, and IAO.
>>
>> -*GGO Genome term design*: Use NCBITaxon to represent organism
>> taxonomy terms and hierarchy. The GGO genome term IRIs are generated
>> by mapping the IDs to the NCBITaxon term IRIs. With this design, the
>> GGO genome term IRIs are predefined based on NCBITaxon records.
>>
>> -*GGO Gene term design*: Extract the information from the NCBI Gene
>> Database and use the information to represent gene information. The
>> mapping between NCBI GeneID and GGO gene IDs will be made, so that
>> GGO gene term IRIs are predefined based on NCBI GeneIDs.
>>
>> -Here is the statistics of current GGO:
>> http://www.ontobee.org/ontostat.php?ontology=GGO
>>
>> Here is some specific explanation:
>>
>> *GGO term prefix*: GGO term IRIs are generated usign the prefix "GGO_"
>> followed by 10 digital numbers.
>>
>> Two key terms:
>>
>> -GGO 'genome': GGO ID: GGO_0000000001
>>
>> -GGO 'gene': GGO ID: GGO_0000000002
>>
>> *Specific GGO genome term*: For each GGO genome term, use the
>> following
>> pattern:
>>
>> * *Label*: "genome of [NCBITaxon lable]"
>> * *GGO ID*: "GGO_{1000000000 + taxon ID}"
>> * *Hierarchy*: follow the same hierarchy as shown in NCBITaxon
>> * *Example*: for human (homo sapiens; NCBITaxon_NCBITaxon_9606):
>>
>> o GGO genome term label: 'genome of Homo sapiens'
>> o GGO IRI: "GGO_{1000000000 + 9606}" = 'GGO_1000009606'
>>
>> *For general GGO gene term*: For each GGO gene term, use the
>> following
>> pattern:
>>
>> * *Label*: "gene of [NCBITaxon lable]"
>> * *GGO ID*: "GGO_{2000000000 + taxon ID}"
>> * *Hierarchy*: follow the same hierarchy as shown in NCBITaxon
>> * *Example*: for human (homo sapiens; NCBITaxon_NCBITaxon_9606):
>>
>> o GGO genome gene term label: 'gene of Homo sapiens'
>> o GGO IRI: "GGO_{2000000000 + 9606}" = 'GGO_2000009606'
>>
>> *For specific GGO gene term: *For each specific GGO gene term, use
>> the following pattern:
>>
>> * *Label*: add the gene symbol as provided by NCBI Gene database.
>> * *GGO ID*: "GGO_{3000000000 + NCBI GeneID}"
>> * *Hierarchy*: position under the "gene of NCBITaxon label" as shown
>> above.
>> * *Example*: for human gene TP53 p53 that has GeneID of 7157
>> <http://www.ncbi.nlm.nih.gov/gene/7157>:
>>
>> o GGO specific gene term label: 'TP53' (the official gene symbol)
>> o GGO gene term synonyms: use the synonyms provided by the
>> NCBI Gene database.
>> o GGO IRI: "GGO_{3000000000 + 7157}" = 'GGO_3000007157'
>> o See:
>>
>> http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibra
>> ry.org/obo/GGO_3000007157
>>
>> <http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibr
>> ary.org/obo/GGO_3000007157>
>>
>> o Check an E. coli example:
>>
>> http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibra
>> ry.org/obo/GGO_3000006647
>>
>> <http://www.ontobee.org/browser/rdf.php?o=GGO&iri=http://purl.obolibr
>> ary.org/obo/GGO_3000006647>
>>
>>
>> As seen on the above two samples, for each specific gene, GGO has
>> included many attributes retrieved from the NCBI Gene database, such
>> as gene symbol and synonyms, GeneID, locus tag and other database
>> cross reference IDs, gene annotation, gene type, … We plan to add
>> more information later.
>>
>> Note that with the above design, we have predefined about one million
>> of GGO genome IDs (since NCBOTaxon has about 1 mill terms), and over
>> 10 million of GGO gene IDs (since over 10 mill NCBI Gene IDs exist).
>> I am happy to provide more information later about the GGO rationale
>> and development strategy.
>>
>> As an aside: with the GGO support, we can now query Ontobee for human
>> or E. coli genes, such as:
>>
>> Search human genes containing “TP53”:
>>
>> http://www.ontobee.org/browser/index.php?keywords=TP53&Submit2=Search
>> +terms&o=GGO
>> <http://www.ontobee.org/browser/index.php?keywords=TP53&Submit2=Searc
>> h+terms&o=GGO>
>>
>>
>> Search human genes containing “sod1”:
>>
>> http://www.ontobee.org/browser/index.php?keywords=sod1&Submit2=Search
>> +terms&o=GGO
>> <http://www.ontobee.org/browser/index.php?keywords=sod1&Submit2=Searc
>> h+terms&o=GGO>
>>
>> In addition, we have developed a software program to automatically
>> generate GGO subset ontology for each genome based on NCBITaxon ID.
>> We will post the results for different genomes of commonly studied
>> organisms in a website soon.
>>
>> Our program to generate a GGO subset for various genes from different
>> genomes is about ready. Our use case is to generate GGO terms and
>> hierarchy for many gene terms from different eukaryotic, prokaryotic,
>> and viral organisms that are curated and collected in the Vaccine
>> Ontology (VO). Currently, those genes collected in VO use VO prefix
>> IDs, which is obviously not optimal. The VO use case is also a
>> motivation for our GGO development. I think different people may have
>> different use cases as well.
>>
>> Relation to other ontologies:
>>
>> -GGO is not like any other existing ontology. GGO is a new ontology
>> that integrates existing non-ontology data particularly the NCBI Gene
>> database data.
>>
>> -GGO vs PRO: GGO represents genomes and genes where a genome includes
>> many genes. GGO is not meant to represent proteins. Proteins are the
>> products of genes and are represented in the Protein Ontology (PRO).
>> Proteins are more complex than genes, at least in eukaryotic systems.
>> Each gene may encode for different proteins, esp. in eukaryotic
>> organisms. We look forward to collaborating with PRO and other
>> ontologies to explore how GGO can link and help ontological protein
>> representation.
>>
>> I believe that GGO will have some great values. GGO will for sure be
>> further developed in different directions. We are happy to discuss
>> with anyone who is interested.
>>
>> Any suggestions and feedback are welcome. Thank you!
>>
>> Oliver
>>
>> Yongqun "Oliver" He, DVM, PhD
>>
>> Associate Professor
>>
>> Unit for Laboratory Animal Medicine
>>
>> Department of Microbiology and Immunology
>>
>> Center for Computational Medicine and Bioinformatics
>>
>> and Comprehensive Cancer Center
>>
>> University of Michigan Medical School
>>
>> Mail: 018 ARF, 1150 W. Medical Center Dr.
>>
>> Ann Arbor, MI 48109
>>
>> Email: yong...@med.umich.edu <mailto:yong...@med.umich.edu>
>>
>> Tel: 734-615-8231 <tel:734-615-8231> (O)
>>
>> http://www.hegroup.org/
>>
>> **********************************************************
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> ----------------------------------------------------------------------
> -------- Android is increasing in popularity, but the open development
> platform that developers love is also attractive to malware creators.
> Download this white paper to learn more about secure code signing
> practices that can help keep Android apps secure.
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________________________________
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