GO wiki (new pages)

Subscribe to GO wiki (new pages) feed
From GO Wiki MediaWiki 1.27.0
Updated: 40 min 26 sec ago

Inferred from Key Residues (IKR)

Wed, 01/10/2018 - 12:35

Vanaukenk: Created page with "IKR: Inferred from Key Residues Updated May 2, 2012 A type of manually-curated evidence derived from sequence analysis, characterized by the lack of key sequence residues. Al..."

IKR: Inferred from Key Residues
Updated May 2, 2012

A type of manually-curated evidence derived from sequence analysis, characterized by the lack of key sequence residues. All annotations that apply this evidence code should use the 'NOT' qualifier. This evidence code is used to annotate a gene product when, although homologous to a particular protein family, it has lost essential residues and is very unlikely to be able to carry out an associated function, participate in the expected associated process, or found in a certain location. This annotation statement can be supported by a published literature reference (e.g. a PubMed identifier) that has described the sequence analysis efforts, or by a GO Reference that describes the process a curator undertook to become sufficiently convinced of the sequence mutation. Where an IKR annotation statement is made using a GO Reference, inclusion of an identifier in the 'with/from' column of the annotation format that can indicate to the user the lacking residues (e.g. an alignment, domain or annotation rule identifier) is absolutely required. In contrast, when an IKR annotation statement is supported by a published literature reference,a value in the 'with/from' field is highly recommended although not required. This evidence code is also referred to as IMR (inferred from Missing Residues).
Examples where the IKR evidence code should be used:

Curator-Determined IKR Annotation Example: Rat HPT (P06866) is homologous to serine proteases and contains a match to the peptidase S1 domain. However further sequence analysis by a curator looking at the the Peptidase S1B, active site established it has lost all essential catalytic residues, making it unable to carry out serine protease activity.
Curator-Determined IKR Annotation Example, Using PAINT : Curators determined that Drosophila neuroligin protein does not have carboxylesterase activity, based on phylogeny-based evidence. The Panther identifier in the 'with/from' field links out to an evidence record citing annotation data from orthologous gene products, supporting the annotation statement.
Paper-Curated IKR Annotation Example: Ross,J., Jiang,H., Kanost,M.R. and Wang,Y. (2003) Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 30;304:117-31 (PMID:12568721). The authors describe the determination of serine protease activity of proteins from the D. melanogaster S1 serine protease gene family, by determining the presence of conserved His, Asp, Ser catalytic triad residues in retrieved sequences. If all three residues were present in the conserved TAAHC, DIAL, and GDSGGP motifs, the sequence was considered to have serine protease activity. Any sequence lacking one of the key residues was identified as an a serine protease homolog, lacking proteolytic activity.
...
2.

DB Object ID

3.

DB Object Symbol

4.

Qualifier

5.

GO ID

6.

DB:Reference

7.

Evidence Code

8.

With/From

...
... P06866 RatHPT NOT GO:0004252serine-type endopeptidase activity GO_REF:0000047 IKR InterPro:IPR000126 ...
... P06866 neuroligin NOT GO:0004091carboxylesterase activity GO_REF:0000033 IKR PANTHER:PTHR11559_AN146 ...
... FB:FBgn0033192 gene S1 NOT GO:0004252serine-type endopeptidase activity PMID:12568721 IKR ...
Examples where the IKR evidence code should not be used:

If there is experimental evidence available from a publication to support a NOT-evidenced annotation. In such instances, the curator should make the IDA, IMP or EXP NOT-qualified annotation based on the experimental evidence. If a paper supplies data that showed the active site was missing and additionally carried out an experimental assay to show lack of activity, it would be correct to create two annotation statements from this paper; both NOT IKR and NOT IDA.
CAUTION: Where curators make judgements of functionning using the IKR evidence code, they should be able to draw on some level of expertise regarding the protein family, as there will always be exceptions to the rule. For instance, Q9H4A3 (WNK1_HUMAN) is a good example where nature has confounded prediction; Cys-250 is present instead of the conserved Lys which is expected to be an active site residue. However Lys-233 appears to fulfill the required catalytic function.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Biological aspect of Descendant (IBD)

Wed, 01/10/2018 - 12:34

Vanaukenk: Created page with "IBD: Inferred from Biological aspect of Descendent Updated May 3, 2011 A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characte..."

IBD: Inferred from Biological aspect of Descendent
Updated May 3, 2011

A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Biological aspect of Ancestor (IBA)

Wed, 01/10/2018 - 12:31

Vanaukenk: Created page with "IBA: Inferred from Biological aspect of Ancestor Updated May 3, 2011 A type of phylogenetic evidence whereby an aspect of a descendent is inferred through the characterizatio..."

IBA: Inferred from Biological aspect of Ancestor
Updated May 3, 2011

A type of phylogenetic evidence whereby an aspect of a descendent is inferred through the characterization of an aspect of a ancestral gene.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Genomic Context (IGC)

Wed, 01/10/2018 - 12:31

Vanaukenk: Created page with "IGC: Inferred from Genomic Context Updated November 9, 2007 operon structure syntenic regions pathway analysis genome scale analysis of processes This evidence code can be us..."

IGC: Inferred from Genomic Context
Updated November 9, 2007

operon structure
syntenic regions
pathway analysis
genome scale analysis of processes
This evidence code can be used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation. Genomic context includes, but is not limited to, such things as identity of the genes neighboring the gene product in question (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis.

IGC may be used in situations where part of the evidence for the function of a protein is that it is present in a putative operon for which the other members of the operon have strong sequence or literature based evidence for function. The presence of the gene in an operon specific for a particular function, pathway, complex, etc. is itself a form of evidence. It is encouraged that when using this code with operon structure that the id numbers for the genes in the operon be put in the with/from field.

The IGC evidence code can also be used to annotate gene products encoded by genes within a region of conserved synteny. For instance, sequence similarity alone may be too low to make an inference but orthology can often be predicted based on the position of a gene within a region of synteny and this used to strengthen the assertion. In these cases the with/from field should be used to store the identity of the positional ortholog.

In the area of process annotations, in order for us to assert that a gene product is involved in a particular process in the cell, that process itself must be happening in that cell. The only way to know if a process is happening is to determine if all of the elements required for that process are present. This is often accomplished by looking to see if there are genes in the genome which can complete every step in the process in question. The same holds true for subunits of protein complexes. This often entails examining many different gene products and many different evidence types found all around the genome of an organism to reach a particular conclusion.

When the method used to make annotations using the IGC code is performed internally by the annotating group and is not published, a short description of the method should be written and added to the GO Consortium's collection of GO references, where it will be given a GO_REF ID which can be used to cite the reference in gene association files.

Usage of the With/From Column for IGC

We recommend making an entry in the with/from column when using this evidence code. In cases where operon structure or synteny are the compelling evidence, include identifier(s) for the neighboring genes in the with/from column. In casees where metabolic reconstruction is the compelling evidence, and there is an identifier for the pathway or system, that should be entered in the with/from column. When multiple entries are placed in the with/from field, they are separated by pipes.

Note that there has been some discrepancy between groups as to the use of the with/from column; please see the Note on Usage of the With/from Column for more details.

...
2.

DB Object ID

3.

DB Object Symbol

4.

Qualifier

5.

GO ID

6.

DB:Reference

7.

Evidence Code

8.

With/From

...
... TIGR_CMR:gene_B_ID gene B GO:0009231 GO_REF:0000025 IGC operon_geneA_ID|operon_geneC_ID (from operon in annotated organism) ...
... TIGR_CMR:gene_A_ID gene A GO:0009102 PMID:15347579 IGC TIGR_GenProp:GenProp0036

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Sequence Model (ISM)

Wed, 01/10/2018 - 12:30

Vanaukenk: Created page with "ISM: Inferred from Sequence Model Prediction methods for non-coding RNA genes such as tRNASCAN-SE, Snoscan, and Rfam Predicted presence of recognized functional domains or mem..."

ISM: Inferred from Sequence Model
Prediction methods for non-coding RNA genes such as tRNASCAN-SE, Snoscan, and Rfam
Predicted presence of recognized functional domains or membership in protein families, as determined by tools such as profile Hidden Markov Models (HMMs), including Pfam and TIGRFAM
Predicted protein features using tools such as TMHMM (transmembrane regions), SignalP (signal peptides on secreted proteins), and TargetP (subcellular localization)
Any other kind of domain modeling tool or collections of them such as SMART, PROSITE, PANTHER, InterPro, etc.
An entry in the with field is required when the model used is an object with an accession number (as found with Pfam, TIGRFAM, InterPro, PROSITE, Rfam, etc.) The with field may be left blank for tools such as tRNAscan and Snoscan where there is not an object with an accession to point to.
The ISM code is a sub-category of the ISS code. The ISM code should be used any time that evidence from some kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Generally, when searching sequences with these modeling tools, the results include statistical scores (such as e values and cutoff scores) that help curators decide when a result is significant enough to warrant making an annotation. If an annotator manually checks these scores and determines if the result makes sense in the context of other information known about the sequence and decides that the evidence warrants a particular annotation, then the evidence code is ISM. However, if a tool that looks only at the scores makes annotations automatically and there is no manual review, the evidence code should be IEA.

It is important to note that some models are more functionally specific than others. In particular this is seen in the profile HMMs and somewhat in PROSITE motifs. Some HMMs are built so that all of the proteins used in building the model and all of the proteins that score well to the model have the exact same function. These models can therefore be used to predict precise functions in match proteins. Other models are built to reflect the shared sequence found among members of superfamiles or subfamilies. These can be used to predict varying levels of functional specificity and may often only provide very general annotations such as identification of a protein as an oxidoreductase. Finally, many models predict the presence of particular domains in a protein which may or may not provide information on the function of a protein, for example the CUB domain is found in a functionally diverse set of proteins and does not allow annotations to function to be made based on its presence alone. Therefore it is very important during the manual annotation process to assess what information it is safe to conclude from a match to any given model.

Some of the sequence-based modeling techniques result in models specific to individual sequence families. The profile HMMs, PROSITE motifs, and InterPro are in this group. In such cases, the with field should be populated with the accession number of the model specific for the functional domain or protein in question. Other sequence-based modeling techniques such as tRNASCAN and Snoscan are methods that result in the prediction of a set of sequences within a particular class (e.g. tRNAs, snoRNAs) and there are not specific models that one can link to each ncRNA. In these cases the with field may be left blank.

If the search for, and evaluation of, the sequence-based model data was described in a published paper, a reference to the paper should be placed in the reference column. However, if the search for and evaluation of the data was performed by the same group that is doing the GO annotation, then a reference should be placed in the reference column that describes the methodology used. If there is no publication for this methodology, a reference can be used from the GO Consortium's collection of GO references; if there is nothing appropriate in this set, the annotating group submit a description of the methods of data collection and evaluation used, and submit it to the GO Consortium. This will be added to the reference collection and will receive a GO_REF accession number for use in annotations.

Examples of when to use ISM

A curator performs an HMM search for a query protein. The result is that the query protein scores above the trusted cutoff to the HMM PF05426 alginate lyase. This HMM describes a family of alginate lyases. After review of all documentation associated with the HMM to determine functional specificity, or lack thereof, of the HMM and review of the scores that the query protein received, if the curator is confident that the query protein is indeed an alginate lyase, the appropriate annotations should be made using ISM as the evidence code, and putting Pfam:PF05426 in the with column. Since this search and evaluation was performed by the curator, a GO standard reference should be used to describe the search and evaluation methods (e.g. GO_REF:0000011).
A paper describes using PROSITE searches with the protein of interest and concludes the protein has a particular binding activity based on a match to a particular PROSITE motif. The curator would make the appropriate GO annotations, using ISM as the evidence code, putting the accession number of the PROSTIE motif that provided the evidence in the with column, and the PMID number of the paper that described the work in the reference column.
A curator runs the program tRNAscan (Lowe, T.M. and Eddy, S.R. NAR, 1997) on a newly sequenced bacterial genome to find the tRNAs. tRNAscan produces a list of the tRNA genes contained within that genome. A curator checks the results of the analysis to make sure that the predictions make sense and are consistent with what is known about the organism. Each of theses genes is given appropriate annotations for a tRNA. The evidence code is ISM, and a reference describing the process the curator used (either a published paper or a GO standard reference) should be placed in the reference column. The with column may be left blank.
PMID:10024243 describes the use of a probabilistic model to predict snoRNA genes in yeast. Each of theses genes may be given appropriate annotations for a snoRNA. The evidence code is ISM, and the reference is the paper describing the work. The with column may be left blank.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Sequence Alignment (ISA)

Wed, 01/10/2018 - 12:29

Vanaukenk: Created page with "ISA: Inferred from Sequence Alignment Sequence similarity with experimentally characterized gene products, as determined by alignments, either pairwise or multiple (tools such..."

ISA: Inferred from Sequence Alignment
Sequence similarity with experimentally characterized gene products, as determined by alignments, either pairwise or multiple (tools such as BLAST, ClustalW, MUSCLE).
An entry in the with field is mandatory.
The ISA code is a sub-category of the ISS code. It should be used whenever a sequence alignment is the basis for making an annotation, but only when a curator has manually reviewed the alignment and choice of GO term or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments (the alignment of two sequences to one another) or multiple alignments (the alignment of 3 or more sequences to one another). BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code. GO policy states that in order to assert that a query protein has the same function as a match protein, the match protein MUST be experimentally characterized. This prevents transitive annotation errors. A transitive annotation error occurs when a protein gets its annotation by virtue of a match to an uncharacterized protein that may itself have gotten its annotation from yet another uncharacterized protein, and so on. With the high number of genome sequences currently in the public databases, the risk of transitive annotation errors is high. However, by requiring that every alignment used for a GO annotation contain an experimentally characterized protein, transitive annotation errors can be significantly reduced.

The process of evaluating a sequence alignment involves checking that the length of the matching region and the percent identity with the matching sequence are sufficient to infer shared function. Residues or secondary structures that are important for function should be conserved. The guiding principle in making sequence similarity based annotations should be that there is a good reason to believe that the comparison is relevant. This evaluation may be carried out by the curator, when sequence analysis is performed by the curators, or by authors of a published paper, when the curator is making annotations based on literature. In literature-based annotation it is incumbent upon the curator to identify which of the proteins in the sequence analysis are experimentally characterized so as to populate the with field.

A note about when to use ISO (inferred from sequence orthology) instead of ISA: If it is known that the experimentally characterized match protein in question is the functional ortholog of the query protein, then the code ISO (Inferred from Sequence Orthology) may be used (see the ISO section below). Orthologs are generally determined from phylogenetic analysis using algorithms such as maximum likelihood or nearest neighbor joining. The presumption is that orthologs often have the same/similar biological function and/or engage in the same or similar biological processes. It can sometimes be difficult to determine when proteins are orthologs of each other, but if one is confident of orthology the orthology specific code should be used.

Note that we have not set definitive numerical cutoffs for the extent or percentage identity of sequence similarity comparisons because groups annotating very different organisms from the current MODs / reference genomes may find that a given arbitrarily selected numerical cutoff does not work when applied to a new organism. It is up to each annotating group to use judgment as to what sequence similarity comparisons are relevant for the purpose of making GO annotations.

It is mandatory to make an entry in the with column when using ISA. The entry in with is the accession number of the experimentally characterized sequences(s) that match the query sequence. Multiple entries in the with field should be separated by pipes. Annotations made with ISA without an entry in the with field will be filtered out by the Annotation File Format Quality Control script which is run monthly.

If the generation and evaluation of the alignment was described in a published paper and then curated by a GO annotator, a reference to the paper should be placed in the reference column. However, if the same group that is doing the GO annotation performed the generation and evaluation of the alignment, then a reference should be placed in the reference column that describes the methodology used. If there is no publication for this methodology, a reference can be used from the GO Consortium's collection of GO references; if there is nothing appropriate in this set, the annotating group submit a description of the methods of data collection and evaluation used, and submit it to the GO Consortium. This will be added to the reference collection and will receive a GO_REF accession number for use in annotations.

Examples of when to use ISA:

A curator generates a pairwise alignment between a query Haemophilus influenzae protein that he/she is trying to annotate and a Vibrio marinus protein. The curator sees that the Vibrio protein is experimentally characterized. The curator evaluates the alignment and sees that the two proteins match over nearly their entire lengths at 68% identity. Furthermore, after reading information on the characterized Vibrio protein the curator looks for the important residues needed for catalysis and binding in the Vibrio protein and finds that they are conserved in the Haemophilus protein. The curator reads the available literature on the Vibrio protein to determine what is known about that protein. The curator can then assign GO terms to the Haemophilus protein based on what has been experimentally determined in the Vibrio protein. The code for this annotation is ISA, the accession number of the Vibrio protein should be placed in the with field. If the process used by the curator for evaluation of the sequence alignments is not in a published paper they should refer to a GO standard reference, for example GO_REF:0000012.
A curator performs sequence similarity analysis on a group of genes, (e.g. sequence similarity alignments of the human NDUFS8 gene (UniProtKB accession: O00217) with several other genes) and identifies several genes with very high sequence identity to the experimentally characterized human HDUFS8 gene: orangutan and chimpanzee (both 100% sequence identity), crab-eating macaque (95% identity), and gorilla (92% identity). The curator judged that these high sequence matches to the human sequence meant that all proteins possessed a similar function, therefore, annotations were made for the related genes in orangutan (UniProt:Q5RC7), macaque (UniProt:Q60HE3), chimpanzee (UniProt:Q0MQI3), and gorilla (UniProt:Q0MQI2) by ISS with the experimentally characterized human NDUFS8 protein, and the accession number of the human NDUFS8 gene was included in the with column for each of these annotations. As there is no published paper describing this sequence analysis, the id of the GO_REF (e.g. GO_REF:0000024) that describes the process the curator carried out to make this judgment is placed in the REF_DB_ID field.
PMID:2165073 identifies a new gene, AAC3, that is similar to two known genes of the same species (S. cerevisiae) based on Southern hybridization. Cloning and sequencing of the new AAC3 gene indicates that it is similar to the previously characterized ADP/ATP translocators AAC1 and PET9. For the AAC3 gene, an annotation may be made to the function term ATP:ADP antiporter activity using the evidence code ISA; the reference is the paper which performed the analysis and the accession numbers of the experimentally genes with which AAC3 was aligned (AAC1 and PET9) should be placed in the with field.
PMID:12507466 describes a set of proteins containing both experimentally confirmed and predicted N-terminal acetyltransferases (NATs) that were collected and assigned to orthologous groups based on phylogenetic analysis. Three of the groups, Ard1, Mak3, and Nat3, were named based on the well characterized gene by that name from S. cerevisiae that is a member of the group. In addition, a previously unknown group with unknown substrate specificity was identified, called Nat5 based on the name of the S. cerevisiae member of the group. About the Nat5 family, the authors make this statement Nat5p represents a family of the putative NATs with orthlogous proteins identified in yeast, S. pombe, C. elegans, D. melanogaster, A. thaliana and H. sapiens. The finding of this new family is only based on sequence similarity of Nat5p (YOR253Wp) to other NATs. Our attempts to detect any Nat5p substrates in yeast by 2D-gel electrophoresis has been so far unsuccessful, but this may reflect the rarity of the substrates in vivo or that Nat5p is acting on the smaller polypetides with mobility parameters undetectable by our regular 2D-gel procedure. As a protein with sequence similarity to other NATs, the annotation that may be made for NAT5 is to the function term peptide alpha-N-acetyltransferase activity. Although this paper clearly discussed orthology relationships, the evidence code for this annotation for NAT5 is ISA because it is not based on the orthology relationship, but merely on similarity with the other experimentally characterized NATs in yeast, MAK3, ARD1, and NAT3, and the accession numbers of these three genes should be placed in the with field. The reference is the paper which performed the analysis, Note that this paper may also be used for annotations using the ISO code when the annotation is based on the orthology relationships described in the paper.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Sequence Orthology (ISO)

Wed, 01/10/2018 - 12:28

Vanaukenk: Created page with "ISO: Inferred from Sequence Orthology Pairwise or multiple alignments between a query protein and experimentally characterized match proteins when the proteins are established..."

ISO: Inferred from Sequence Orthology
Pairwise or multiple alignments between a query protein and experimentally characterized match proteins when the proteins are established to be orthologs of each other.
Phylogenetic analysis of a set of proteins to define orthologous groups.
An entry in the with field is mandatory.
The ISO code is a sub-category of the ISS code. Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following:

phylogenetic analysis
coincident expression
conserved map location
functional complementation
immunological cross-reaction
similarity in subcellular localization
subunit structure
substrate specificity
response to specific inhibitors
It should be noted that there are known cases where a gene in one organism is significantly different in size from its ortholog(s) in other species. For example, the U2 snRNA in S. cerevisiae is much larger than vertebrate U2 snRNAs due to several additional domains. However it has been shown that both S. cerevisiae and vertebrate U2 snRNAs have the same conserved core and perform the same basic role in the spliceosome, even though a simplistic sequence comparison might miss this due to the large size difference between U2 in S. cerevisiae and U2 in mammalian species.

When making an annotation using the ISO evidence code, an entry in the with field is mandatory. This entry will be the accession number of an experimentally characterized orthologous gene product. The matching orthologous gene product must have substantiating experimental evidence to support the annotation. In addition, there will be cases where a gene product in one species is the ortholog of several closely related paralogous genes in another species. In these cases, the ID for all of these paralogs should be included in the with field. Annotations made with ISO without an entry in the with field will be filtered out by the Annotation File Format Quality Control script.

If the paper being used to make the annotation demonstrates the orthology, then that paper is used as the reference for that annotation. However, if the group doing the annotation is establishing orthology and there is no published reference, a reference can be used from the GO Consortium's collection of GO references; if there is nothing appropriate in this set, the annotating group submit a description of the methods of data collection and evaluation used, and submit it to the GO Consortium. This will be added to the reference collection and will receive a GO_REF accession number for use in annotations. For e.g., GO_REF:0000096 describes MGI's practice of transferring experimental GO annotations from rat and human to mouse genes based on orthology evidence (i.e. ISO).

It is important to note that if revised predictions on orthologous protein sets are produced at a later time than the original annotation, annotations should be updated accordingly.

Example of when to use ISO:

PMID:12507466 describes a set of proteins containing both experimentally confirmed and predicted N-terminal acetyltransferases (NATs) that were collected and assigned to orthologous groups based on phylogenetic analysis. Three of the groups, Ard1, Mak3, and Nat3, were named based on the well characterized gene by that name from S. cerevisiae that is a member of the group. Proteins in these orthologous groups without experimental characterization can be assigned the function term peptide alpha-N-acetyltransferase activity based on orthology to the experimentally characterized proteins within the orthologous group. The evidence code for this annotation is ISO, the reference is the paper which performed the analysis, and the accession numbers of the experimentally characterized members of the orthologous group should be placed in the with field. The paper also makes it clear that the genes, ARD1, MAK3, and NAT3 are well characterized experimentally, thus one could use the relevant one of these genes in the with field for annotations of members of their orthology groups without further reading. There may be additional characterized genes in each group, but it is not obvious from the paper. Also note that this paper also describes a putative Nat5 family only based on sequence similarity of Nat5p (YOR253Wp) to other NATs. As there is no experimentally characterized member of the Nat5 family, no annotations may be made based on the Nat5 orthology grouping, though see the ISA section for a description of the annotation which may be made for NAT5.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Sequence or structural Similarity (ISS)

Wed, 01/10/2018 - 12:10

Vanaukenk: Created page with "ISS: Inferred from Sequence or Structural Similarity Updated April 1, 2008 The ISS evidence code or one of its sub-categories should be used whenever a sequence-based analysi..."

ISS: Inferred from Sequence or Structural Similarity
Updated April 1, 2008

The ISS evidence code or one of its sub-categories should be used whenever a sequence-based analysis forms the basis for an annotation and review of the evidence and annotation has been done manually. If the annotation has not been reviewed manually, the correct evidence code is IEA, even if the evidence supporting the annotation is all sequence based. ISS should be used if a combination of sequence-based tools or methods are used. If only one particular type of sequence-based evidence is used then one of the more specific sub-categories of ISS may be more appropriate for the annotation. There are three specific sub-categories of ISS, mentioned briefly here and described in more detail below:

ISA: If the primary piece of evidence is a pairwise or multiple alignment then ISA (Inferred from Sequence Alignment) would likely be the appropriate evidence code to use.
ISO: If the primary piece of evidence is the assertion of orthology between the gene product and a gene product in another organism, ISO (Inferred from Sequence Orthology) would likely be the appropriate evidence code to use.
ISM: If any kind of sequence modeling method (e.g. Hidden Markov Models) is the primary piece of evidence then the ISM (Inferred from Sequence Model) code is the most appropriate.
ISS can also be used for structural similarity with experimentally characterized gene products, as determined by crystallography, nuclear magnetic resonance, or computational prediction. In practice, ISS annotations are rarely, if ever, made purely from structural information. When included, structural information is generally at the level of secondary structure modeling or prediction derived from sequence information. Secondary structure information is particularly useful as one component of RNA gene predictions and in some domain models.

Population of the with field is important when using the ISS code or one of its sub-categories. The entry in with is the accession of the object or model to which your query has similarity. It is mandatory for annotators to make an entry in the with field when using the ISS code or one of its sub-categories if the annotation is based on an alignment with other proteins (e.g UniProt) or a sequence model contained in a database (e.g. Pfam, InterPro). If the annotation is based on a method such as tRNASCAN, which cannot be referred to with an accession number, the with field may be left empty. Entries in the with field should be in the format database:accession, where database is one of the abbreviations listed in the GO database abbreviations collection and accession is the accession number of the object the sequence similarity is with. Multiple entries in the with field should be separated by pipes.

If the searches and evaluation of the sequence-based data are described in a published paper, the ID (either one assigned by PubMed or one assigned by another database such as a Model Organism Database) of the paper should be placed in the reference column. However, if the group that is doing the GO annotation performed the searches and evaluation of the sequence-based data, and there is no published reference, a reference can be used from the GO Consortium's collection of GO references; if there is nothing appropriate in this set, the annotating group submit a description of the methods of data collection and evaluation used, and submit it to the GO Consortium. This will be added to the reference collection and will receive a GO_REF accession number for use in annotations. In all cases, the ID of the reference describing the methodology of the sequence analysis should be placed in the reference column.

Examples of when to use ISS:

An ISS annotation is often based on more than just one type of sequence-based evidence. Often, a host of searches are performed for any given query protein. These searches might include BLAST, profile HMMs, TMHMM, SignalP, PROSITE, InterPro, etc. Evaluation of output from these search tools (bear in mind that every search may not yield results for every protein) leads an annotator to a particular ISS annotation for a particular protein. For example, a BLAST search might reveal that a query protein matches an experimentally characterized protein from another species at 50% identity over the full lengths of both proteins. After reading literature about the match protein, the curator sees that the match protein is known to contain a domain located in the plasma membrane and another domain that extends into the cytoplasm. It is also known from the literature that the experimentally characterized match protein requires the binding of ATP to function. TMHMM analysis of the query protein predicts several membrane spanning regions in one half of the protein (consistent with location in a membrane). In addition there are PROSITE and Pfam results which reveal the presence of an ATP-binding domain in the other half of the protein which TMHMM predicts to be cytoplasmic. These four search results taken together point to a probable identification of the query protein as having the function of the match protein.
PMID:8674114 describes comparative analysis of several newly identified and previously characterized snoRNAs. They list a number of sequence features, both conserved sequence elements and a region of complementarity to rRNA, and spacings that are characteristic of box C/D snoRNAs. As the authors don't develop a predictive method, the analysis they describe isn't considered to be a model, so ISM is not appropriate. As being a member of the box C/D snoRNA family is predictive for being a methylation guide, one could make annotations for a number of snoRNAs based on this paper. Note that the yeast U24 gene (snR24) is also experimentally characterized in this paper. Thus, for snR24 from S. cerevisiae, it is possible to make annotations using both the ISS and the IMP evidence codes, or one might choose not to make the ISS-based annotation for snR24 since experimental evidence is available.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Expression Pattern (IEP)

Wed, 01/10/2018 - 12:09

Vanaukenk: Created page with "IEP: Inferred from Expression Pattern Updated November 9, 2007 Transcript levels or timing (e.g. Northerns, microarray data) Protein levels (e.g. Western blots) The IEP evide..."

IEP: Inferred from Expression Pattern
Updated November 9, 2007

Transcript levels or timing (e.g. Northerns, microarray data)
Protein levels (e.g. Western blots)
The IEP evidence code covers cases where the annotation is inferred from the timing or location of expression of a gene, particularly when comparing a gene that is not yet characterized with the timing or location of expression of genes known to be involved in a particular process. Use this code with caution! It may be difficult to determine whether the expression pattern really indicates that a gene plays a role in a given process, so the IEP evidence code is usually used in conjunction with high level GO terms in the biological process ontology.

Note that we have not yet encountered any examples where we feel it is valid to make annotations to terms from the cellular component or molecular function ontologies on the basis of expression pattern data. Thus we currently recommend that this code be restricted to annotations to terms from the biological process ontology. Also, different annotating groups use different identifiers (gene or protein or gene_product) and no inference should be made as to whether an annotation made using IEP concerns a gene, RNA or protein.

Examples where the IEP evidence code should be used:

genes upregulated during a stress condition may be annotated to the process of stress response (for example, heat shock proteins)
genes selectively expressed at specific developmental stages in specific organs may be annotated to xxx development
Example annotations:

PMID:10748035. Both mRNA and protein levels of Atp2a2 (SERCA2) are increased upon ER stress in a pattern highly similar to BiP, a well-characterized endoplasmic reticulum (ER) chaperone with a role in the ER stress response. Therefore Atp2a2 may be annotated to 'response to endoplasmic reticulum stress' with IEP.
PMID:17627301. Primate IRF2BPL (EAP1) expression increases selectively at puberty in the hypothalamus, and IRF2BPL is expressed in neurons involved in the inhibitory and facilitatory control of reproduction. Ideally there should be additional support for a role of the gene product in the process. In this example, PMID: 17627301 shows that human IRF2BPL (EAP1) activates genes required for reproductive function, and represses inhibitory genes. Therefore primate IRF2BPL may be annotated to 'development of secondary female sexual characteristics' with IEP.
Examples where the IEP evidence code should not be used:

Function and component annotations should not be made with IEP.
Exogenous expression or overexpression of a gene should be not annotated using IEP; only the normal expression pattern should lead to an IEP annotation.
Overexpression of a gene causing increased activity of an enzyme should be annotated to IDA or IMP (see IDA documentation)
Overexpression (wild type or mutated) of a gene causing an abnormal phenotype should be annotated to IMP
Exogenous expression of a gene and assaying of its function should be annotated to IDA (like a transcription factor)
Binding assays with overexpressed proteins or exogenously expressed proteins should be annotated to IPI for protein binding or IDA for binding to other molecules.
Observation of protein localization for a component annotation should be made using the IDA evidence code.
Annotation to the molecular function term transcription factor activity where the experimental evidence is that introduction of the gene to be tested into an in vitro assay system leads to expression of the appropriate reporter gene. Annotate using the IDA evidence code.
Annotation to a binding molecular function term, e.g. calmodulin binding, where the experiment was to screen an expression library (a library expressing various proteins) to identify which of the library proteins interact with a particular protein of interest. Annotate using the IPI evidence code with the accession number of to the interacting protein (or its corresponding gene) in the with/from field.
Annotating an enzymatic function to a Molecular Function Term based on an overexpression experiment. Since this is not the normal expression pattern, the IEP code does not apply. IDA would be the appropriate evidence code for this annotation. Annotating guanylate cyclase 2f from rat (GC-F), to the Molecular Function term guanylate cyclase activity, based on the experimental result that over-production of GC-E and GC-F in COS cells resulted in production of or increase in of guanylyl cyclase activity (PMID:7831337). IDA would be the appropriate evidence code for this annotation.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Genetic Interaction (IGI)

Wed, 01/10/2018 - 12:09

Vanaukenk: Created page with "IGI: Inferred from Genetic Interaction Updated March 1, 2016 Genetic interactions involving two or more mutations that result in suppression or enhancement of a given phenoty..."

IGI: Inferred from Genetic Interaction
Updated March 1, 2016

Genetic interactions involving two or more mutations that result in suppression or enhancement of a given phenotype, also synergistic (synthetic) interactions
Co-transfection experiments in which two or more genes are expressed in a heterologous system to assess functional interaction
Expression of one gene alters the phenotypic outcome of a mutation in another gene; the two genes may or may not be from the same species. In the literature, these types of experiments are variably referred to as: functional complementation, rescue experiments, or suppression
The IGI evidence code is used for annotations based on experiments reporting the effects of perturbations in the sequence or expression of one or more genes or gene products. IGI is also used for experiments that interrogate functional interactions between two or more genes or gene products when co-expressed, for example, in a cell line. Additional uses of IGI include experiments in which the expression of one gene affects the phenotypic outcome of a mutation in another gene.

Key to deciding whether or not to use the IGI or IMP (Inferred from Mutant Phenotype) evidence code is consideration of the point of reference (i.e., what is being compared) to determine a possible interaction. If experiments interrogate the effects of multiple mutations or differences from the control, then use IGI. If experiments interrogate the effects of a single mutation or difference from the control, then use IMP.

The IGI evidence code requires curators enter a stable database identifier for the interacting entity in the With/From field of the Gene Association File (GAF). Independent interactors may be captured in the With/From field by separating each entry with a pipe. If the interaction experiment involves multiple perturbations simultaneously, e.g. triply mutant strains, then the respective interactors are separated with a comma.

Examples where the IGI evidence code should be used:

Genetic interactions such as suppression, enhancement, synergistic (synthetic) interactions, etc.

This use of the IGI evidence code refers to the more “traditional” genetic interaction experiments performed in model organisms, such as Saccharomyces cerevisiae, as well as more recent approaches adopted in a number of different systems such as RNA-mediated knockdown or genome editing techniques. Note that genetic interaction experiments may be performed with both loss-and gain-of-function mutations. Consequently, curators will need to use their expertise to determine whether interaction phenotypes resulting from gain-of-function mutations are informative about the normal, wild type role of a gene or gene product.

Example 1: Double loss-of-function mutations resulting in enhancement of a mutant phenotype
Localized cell wall degradation is essential for proper cell fusion in the fission yeast, Schizosaccharomyces pombe. This process is accomplished by the localized action of degradative enzymes including several distinct glucanases that act on differentpolysaccharides. Deletion of multiple glucanases in S. pombe results in decreasing efficiency of cell fusion indicating thateach enzyme contributes additively to this process.
exg3 fungal-type cell wall disassembly involved in conjugation with cellular fusion (GO:1904541) PMID:25825517 IGI agn2
agn2 fungal-type cell wall disassembly involved in conjugation with cellular fusion (GO:1904541) PMID:25825517 IGI exg3
Example 2: Gain-of-function mutation
The response to axonal injury requires the activities of MAP kinase and cAMP signaling pathways that are required, for example, for signaling growth cone formation. In C. elegans, the activity of the upstream-most kinase in one of the MAPK signaling pathways, DLK-1, is stimulated by Ca2+ influx mediated by the EGL-19 voltage-gated calcium channel. EGL-19’s regulatory role in the MAPK-mediated axon regeneration pathway was determined, in part, through doubly mutant animals containing an egl-19 hypermorphic mutation that results in occasional action potentials with significantly prolonged plateau phases and a dlk-1 loss-of-function mutation that showed a reduced axon regenerative response when compared to egl-19 alone.
EGL-19 positive regulation of MAPK cascade involved in axon regeneration (GO:1904922) PMID:20203177 IGI DLK-1
Note that in this example, reciprocal IGI annotations are not made, as the GO term selected for EGL-19 does not make sense for DLK-1.
Example 3: Synergistic (synthetic) interactions
Disruption of the MSB2 gene in S. cerevisiae has no appreciable effects on the cell's ability to activate the High-Osmolarity Glycerol (HOG) pathway upon osmotic stress, or on cellular growth on high-osmolarity media. To identify potential osmosensors in the SHO1 branch of the HOG pathway, the authors screened for a mutant that is osmosensitive only in an msb2Δ background and recovered mutations in the HKR1 gene. Like MSB2, mutations in HRK1 alone confer no osmosensitivity to the cells.
MSB2 hyperosmotic response (GO:0006972) PMID:17627274 IGI HKR1
HKR1 hyperosmotic response (GO:0006972) PMID:17627274 IGI MSB2
Co-transfection experiments

Co-transfection experiments include those experiments where two or more gene products are expressed in a heterologous system, such as a cell line, for the purposes of interrogating a functional interaction between them.

Example 1: Co-transfection of G protein-coupled receptors (GPCRs)
In C. elegans, the response to dauer pheromone, a mixture of small molecules, is mediated by G protein-coupled receptors (GPCRs). Genetic analysis has implicated two GPCRs, SRBC-64 and SRBC-66, in a signaling pathway that responds to specific components of dauer pheromone. To assess the biochemical role of SRBC-64 and SRBC-66, the gene products were expressed singly or in combination in HEK293 cells. Only when expressed in combination were the GPCRs able to enhance forskolin-stimulated cAMP production.
SRBC-64 G-protein coupled receptor signaling pathway (GO:0007186) PMID:19797623 IGI SRBC-66
SRBC-66 G-protein coupled receptor signaling pathway (GO:0007186) PMID:19797623 IGI SRBC-64
Expression of one gene affects the phenotype of a mutation in another gene

These types of experiments are described in various ways in the published literature, but generally involve expressing a wild-type copy of one gene in the background of a mutation in a second, different gene to determine if the expressed gene can mask the phenotype of the mutated gene. The two genes may or may not be from the same species. When genes from different species are analyzed it is often with the intent of demonstrating functional conservation between species.

Example 1: Genes from different species
C. elegans contains two genes, lgg-1 and lgg-2, with sequence similarity to the Saccharomyces cerevisiae ubiquitin-like protein Atg8 that is required for autophagosome biogenesis. Transformation of lgg-1, but not lgg-2, into atg8 deletion mutants in nitrogen starvation medium results in increased survival compared to atg8 mutants alone, indicating that lgg-1 can functionally complement budding yeast atg8.
lgg-1 (C. elegans) macroautophagy (GO:0016236) PMID:20523114 IGI atg8 (S. cerevisiae)
For these annotations, the With/From column should list the identifier for the endogenous gene that is complemented by the heterologously expressed gene being annotated. In annotations from cross-species functional complementation experiments, the gene referred to in the With/From column will thus be from a different species than the gene being annotated.
Example 2: Different genes from the same species
The planar cell polarity pathway is critical for a number of biological processes including epidermal wound repair. Activity of the GRHL3 transcription factor is essential for efficient wound repair in mice and human cell lines. Wound repair requires activation of the RhoA small GTPase to effect the cellular polarization, actin polymerization and epidermal migration critical to wound closure. The gene encoding the RhoGEF RhoGEF119, a RhoA GTPase activator, is a transcriptional target of GRHL3, and RHOGEF119 activity is also required for wound repair. Expression of human RhoGEF119 in human Grhl3-kd cell lines rescues the actin polymerization defects resulting from loss of Grhl13, indicating a role for RhoGEF119 in regulation of actin cytoskeletal organization during wound repair.
ARHGEF19 positive regulation of actin cytoskeleton organization (GO:0032956) PMID:20643356 IGI GRHL3
GRHL3 positive regulation of actin cytoskeleton organization (GO:0032956) PMID:20643356 IGI ARHGEF119
Note that rescue experiments may be used to help determine the order in which gene products act within a biological pathway or process.
Example 3: Different genes from the same species
Localized assembly of a filamentous actin (F-actin) network at the leading edge of D. discoideum cells is required for proper chemotaxis towards the cAMP chemoattractant. The organization of actin filaments is regulated by intracellular pH; an increase in pH is necessary for chemotaxis and required the Na+/H+ exchanger Ddnhe1. Expression of DdAip1, the D. discoideum ortholog of Actin-interacting protein 1, suppresses the chemotaxis defect of Ddnhe1 mutants by restoring the F-actin network, thus illustrating DdAip1's role in actin filament polymerization.
aip1 actin filament polymerization (GO:0030041) PMID:20668166 IGI nhe1
When NOT to use IGI

A mutation in one gene affects some property of another gene

Some experiments assess a functional interaction between one or more gene products by examining the effects that mutations in one gene have on the properties of another. These types of experiments are annotated using the IMP (Inferred from Mutant Phenotype) evidence code and the target, or affected gene product, may be captured as an Annotation Extension. The key here is that the genetic perturbation is directed at only one of the gene products in the experiment.

For example, treatment of cells with GSK3B antagonists results in nuclear accumulation of the GATA6 transcription factor. This experiment indicates that GSK3B negatively regulates GATA6 localization.
GSK3B negative regulation of protein localization to nucleus (GO:1900181) PMID:23624080 transports_or_maintains_localization_of GATA6
Expression of a gene is used to restore the normal function of the same gene

Evidence for a gene's role in a given biological process can be evaluated by expression of a wild-type copy of the gene to "rescue" the phenotype of a mutation in that gene. These experiments, since they involve the same gene, are not considered genetic interactions and may instead be used to support an IMP annotation.

For example, loss-of-function mutations in the C. elegans phosphoinositol-5-phosphatase inpp-1 exhibit defective Ca2+ signaling in the AWA chemosensory neuron in response to odorant stimulus. Expression of inpp-1 from a genomic fosmid clone or from an AWA-specific promoter restores the wild-type AWA-mediated odorant response.
inpp-1 response to odorant (GO:1990834) IMP
Expression of a miRNA affects expression of a target gene as determined via a reporter assay

A reporter assay is a common way to determine the target(s) of a miRNA. The 3'UTR of an mRNA containing specific miRNA binding sites fused to a reporter gene is transfected into cells together with the miRNA. If the mRNA is a bona fide target the miRNA binds to and reduces the expression of the reporter gene. The assay is assessing the action of the miRNA on the target, not how the two entities work together to affect some process, therefore the evidence code should not be IGI. Since the effect of the miRNA can be determined without any perturbation, the evidence code used is IDA. Often the authors will perform a perturbation experiment as well, but this is not required to see the effect of the miRNA on the target.

For example, in luciferase reporter assays with a construct containing a full-length Snai1 3′UTR sequence, miR-133 transfection strongly repressed the luciferase activity by 60%. Mutations of either predicted miR-133-binding site in the Snai1 3′UTR reduced the responsiveness to miR-133, which was almost absent with mutations of both sites, suggesting direct binding of miR-133 to both sites (Fig​.4C).
Human miR-133a mRNA binding involved in posttranscriptional gene silencing (GO:1903231) PMID:24920580 IDA has_direct_input SNAI1
Human miR-133a gene silencing by miRNA (GO:0035195) PMID:24920580 IDA regulates_expression_of SNAI1

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category: Evidence Codes]] Vanaukenk
Categories: GO Internal

Inferred from Mutant Phenotype (IMP)

Wed, 01/10/2018 - 11:52

Vanaukenk:

IMP: Inferred from Mutant Phenotype
Updated November 9, 2007

mutations, natural or introduced, that result in partial or complete impairment or alteration of the function of that gene
polymorphism or allelic variation (including where no allele is designated wild-type or mutant)
any procedure that disturbs the expression or function of the gene, including RNAi, anti-sense RNAs, antibody depletion, or the use of any molecule or experimental condition that may disturb or affect the normal functioning of the gene, including: inhibitors, blockers, modifiers, any type of antagonists, temperature jumps, changes in pH or ionic strength.
overexpression or ectopic expression of wild-type or mutant gene that results in aberrant behavior of the system or aberrant expression where the resulting mutant phenotype is used to make a judgment about the normal activity of that gene product.
The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible.

For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the annotator should use the author's intent and interpretation of the experiment as a guide as to whether IMP or IDA is appropriate. When the author is comparing differences between alleles, regardless of the simplicity or complexity of the assay, IMP is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, IDA is appropriate. Examples where the IMP code should be used

use of an inhibitor of a gene product's activity in order to see the effect of absence, or significant depletion, of that gene product. For example, an experiment using baicalein to inhibit the activity of 12-LOX in a murine bladder cancer cell line inhibits cell proliferation in a concentration dependent manner (see PMID:15161019) results in an annotation to the GO term cell proliferation using the IMP evidence code for the 12-LOX gene.
transfection into a cell line, overexpression, or extopic expression of a gene where the effects of various alleles of a gene are compared to each other or to wild-type. For this type of experiment, annotate using IMP.
In situations where a mutation in gene A provides information about the function, process, or component of gene B do not use IGI. Use IMP evidence code and use column-16 or the Annotation Extension column to provide additional data. For example, if a mutation in gene A causes a mislocalization of gene B, gene A is annotated to protein localization using IMP and the gene B identifier is added to the Annotation Extension column with the appropriate relationship.
Examples where the IMP code should not be used

mutation in gene B provides information about gene A being annotated. For this type of experiment, use the IGI code.
complementation of a mutation in one organism by a gene from a different organism.
Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used. This is in contrast with a situation where overexpression affects the function or expression of the gene and that difference from normal is used to make an inference about the normal function; in this case use the IMP evidence code.
Usage of the With column for IMP We recommend making a "with" entry in the with/from column when using this evidence code to indicate the identifier for the allele in which the phenotype was observed. When multiple entries are placed in the with/from field, they are separated by pipes. Example for how the with/from column should be filled in

The mouse gene product Actc1 (actin, alpha, cardiac ; MGI:87905), has a GO annotation to muscle thin filament assembly ; GO:0030240, inferred from mutant phenotype, IMP of MGI:2180072 (symbol: Actc1tm1Jll; name: targeted mutation 1, James Lessard), from PMID:9114002. MGI:2180072 is entered in the with/from column for this annotation.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]

[[Category: Annotation]]
[[Category:Evidence Codes]] Vanaukenk
Categories: GO Internal

How to run Mike Cherry's filtering script locally before checking the GAF into SVN?

Wed, 01/10/2018 - 08:34

Vanaukenk:

*You need access to SVN to run the script locally. If you don't have access please write to go-admin@genome.stanford.edu
*Familiarize yourself with SVN commands (http://geneontology.org/page/svn-help)
*You need to check out the following files from SVN. The script will fail or will give you inaccurate reports if you don't have the current version of any of the files.

<pre>

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology
username@ext.geneontology.org's password:
[this will co the entire directory]

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/gene-associations/submission go/gene-associations/submission
username@ext.geneontology.org's password:
[this will co the entire directory]

>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities
username@ext.geneontology.org's password:

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/doc/ go/doc
username@ext.geneontology.org's password:

</pre>

Now you have the necessary files to run the script in your space.

* cd to the gene-associations/submission directory
<pre>
>cd go/gene-associations/submission

>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz

You should see the filtering script report once the script runs through the file.
</pre>


[http://wiki.geneontology.org/index.php/Annotation_Group Back to Annotation Group] Vanaukenk
Categories: GO Internal

Annotation Review Request

Wed, 01/10/2018 - 07:24

Pascale:

* Folder on the GO Google drive: https://drive.google.com/drive/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_
* Create a new spreadsheet for each ticket, according to the template: https://docs.google.com/spreadsheets/d/1sydzUKLMDXexD2vYCumma0VWZsBJZontxDCjAwZ1_hE/edit#gid=0
* Download load the default data from AmiGO and copy the header row from the template
* Name of the file: Ticket-[nnnn] - Review annotations to [GO ID] [TermLabel]
* For requester of the review: If possible, add a suggested action (ie what term to replace by, etc)

* For curators: fill Column 2 and 3: Changed/Removed/Checked (and unchanged) - Git handle of respondent.



[[Category: Annotation]] Pascale
Categories: GO Internal

Ontology meeting 2018-01-15

Mon, 01/08/2018 - 10:43

David: Created page with "No Call due to US Holiday. Category: Ontology Category: Meetings"

No Call due to US Holiday.

[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Ontology meeting 2018-01-08

Fri, 01/05/2018 - 09:43

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 == Editors Discussio..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

== Editors Discussion ==
*The GH ticket-closing jamboree will be from Feb. 12-16th in Denver.
*I have created a page for this meeting here: [[2018 Ontology Editors' GH ticket Meeting]]


= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Ontology editor's conference call minutes Jan-June 2018

Fri, 01/05/2018 - 09:38

David: Created page with "*Jan 8 *Jan 15 *Jan 22 *Jan 29 *Ontology meet..."

*[[Ontology meeting 2018-01-08|Jan 8]]
*[[Ontology meeting 2018-01-15|Jan 15]]
*[[Ontology meeting 2018-01-22|Jan 22]]
*[[Ontology meeting 2018-01-29|Jan 29]]
*[[Ontology meeting 2018-02-05|Feb 5]]
*[[Ontology meeting 2018-02-19|Feb 19]]
*[[Ontology meeting 2018-02-26|Feb 26]]
*[[Ontology meeting 2018-03-05|Mar 5]]
*[[Ontology meeting 2018-03-12|Mar 12]]
*[[Ontology meeting 2018-03-19|Mar 19]]
*[[Ontology meeting 2018-03-26|Mar 26]]
*[[Ontology meeting 2018-04-02|Apr 2]]
*[[Ontology meeting 2018-04-09|Apr 9]]
*[[Ontology meeting 2018-04-16|Apr 16]]
*[[Ontology meeting 2018-04-23|Apr 23]]
*[[Ontology meeting 2018-04-30|Apr 30]]
*[[Ontology meeting 2018-05-07|May 7]]
*[[Ontology meeting 2018-05-21|May 21]]
*[[Ontology meeting 2018-05-28|May 28]]
*[[Ontology meeting 2018-06-04|Jun 4]]
*[[Ontology meeting 2018-06-11|Jun 11]]
*[[Ontology meeting 2018-06-18|Jun 18]]
*[[Ontology meeting 2018-06-25|Jun 25]]





[[Category:Meetings]]
[[Category:Ontology]] David
Categories: GO Internal

2018 Ontology Editors' GH ticket Meeting

Fri, 01/05/2018 - 09:21

David:

= Agenda (Draft) =

== Monday, February 12th ==


== Tuesday, February 13th ==


== Wednesday, February 14th ==


== Thursday, February 15th ==


== Friday, February 16th ==


= Logistics =

== Location==


== Accommodations ==

SpringHill Suites Denver at Anschutz Medical Campus


== Meeting Location ==
University of Colorado Anschutz Medical Campus

* The hotel is across the street from campus.


== Participants ==

{| {{Prettytable}}
|-
! Name
! Organization
! Comments
|-
| David Hill
| The Jackson Laboratory
|
|-
| Kimberly Van Auken
| Caltech
|
|-
| Pascale Gaudet
| SIB Swiss Institute of Bioinformatics
|
|-
|-
| Harold Drabkin
| The Jackson Laboratory
|
|-
| Karen Christie
| The Jackson Laboratory
|
|-
| Judith Blake
| The Jackson Laboratory
|
|-
|}



[[Category:Meetings]]
[[Category:Ontology]] David
Categories: GO Internal

Annotation Conf. Call 2018-01-09

Tue, 01/02/2018 - 07:49

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = = Minutes = *On call: Category:Annotation Working Group"

= Meeting URL =
*https://stanford.zoom.us/j/976175422

= Agenda =

= Minutes =
*On call:




[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Manager Call 2018-01-04

Tue, 01/02/2018 - 07:31

Vanaukenk: /* Agenda */

= Agenda =
*Review draft agenda for docathon
**http://wiki.geneontology.org/index.php/2018_Berkeley_GO_Docathon
*NYU meeting
**Do we have any info on logistics?
**Start working on agenda?

= Minutes =


[[Category:GO Managers Meetings]] Vanaukenk
Categories: GO Internal

Annotation Call 2018 Minutes

Tue, 01/02/2018 - 07:24

Vanaukenk:

* [[Annotation Conf. Call 2018-01-09]]
* [[Annotation Conf. Call 2018-01-23]]
* [[Annotation Conf. Call 2018-02-13]]
* [[Annotation Conf. Call 2018-02-27]]
* [[Annotation Conf. Call 2018-03-13]]
* [[Annotation Conf. Call 2018-03-27]]
* [[Annotation Conf. Call 2018-04-11]]
* [[Annotation Conf. Call 2018-04-25]]
* [[Annotation Conf. Call 2018-05-09]]
* [[Annotation Conf. Call 2018-05-23]]
* [[Annotation Conf. Call 2018-06-13]]
* [[Annotation Conf. Call 2018-06-27]]
* [[Annotation Conf. Call 2018-07-11]]
* [[Annotation Conf. Call 2018-07-25]]
* [[Annotation Conf. Call 2018-08-08]]
* [[Annotation Conf. Call 2018-08-22]]
* [[Annotation Conf. Call 2018-09-12]]
* [[Annotation Conf. Call 2018-09-26]]
* [[Annotation Conf. Call 2018-10-10]]
* [[Annotation Conf. Call 2018-10-24]]
* [[Annotation Conf. Call 2018-11-14]]
* [[Annotation Conf. Call 2018-11-28]]
* [[Annotation Conf. Call 2018-12-12]]

[[Category: Annotation]] [[Category:Working Groups]] Vanaukenk
Categories: GO Internal