Deletion log
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Below is a list of the most recent deletions.
- 17:57, 19 April 2024 Pascale talk contribs deleted page AmiGO 2 Manual: Linking (content was: "See newer documentation on https://geneontology.org/docs/faq/ AmiGO 2 now offers a stable set of URLs for linking. This page contains the supported methods for linking into AmiGO 2. Users may also be interested in some of the more RESTy aspects of AmiGO 2 or the possibility of incorporating the widgets and int...", and the only contributor was "Sjcarbon" (talk))
- 11:35, 13 February 2024 Pascale talk contribs deleted page Indirectly localizes (content was: "Category:Deprecated =This relation is deprecated in GO.= ==Definition== Identifies the gene product or substance whose location is established or maintained a process in which the annotated gene product is involved, but where the annotated gene product is known not to act directly. ==Child terms== * None. ==Annotation Extension Usage Examples==")
- 10:43, 13 February 2024 Pascale talk contribs deleted page Has participant (content was: "This relation is not used in GO extensions. Consider Has_input or Has_output ==Definition== Identifies an entity affected by the gene product's participation in a molecular function or biological process ==Cross-reference to Relations Ontology (RO) term== [http://purl.obolibrary.org/obo/RO_0000057 RO:0000057 has participant] ---- Date last Reviewed: 2021-12-15 Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extensi...")
- 11:31, 23 January 2024 Pascale talk contribs deleted page File:Precomposed term replacement.png (Deleted old revision 20240123152520!Precomposed_term_replacement.png)
- 04:46, 18 January 2024 Pascale talk contribs deleted page Microbial ontology development and annotation (content was: "Category:Ontology ===Staff=== Lead by: Suzi Others: Jane, Pascale, Michelle, Jim Hu ? ===Contacts=== '''Bruno Sobral''', Virginia Bioinformatics Institute [http://patric.vbi.vt.edu/ Pathogen Portal, PathoSystems Resource Integration Center (PATRIC)] '''Philippe le Mercier''' SIB, [http://www.expasy.ch/viralzone/ ViralZone] '''Jonathan Eisen''' UCD [http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page his project's wiki] '''Simon Kasif''' Boston Univer...")
- 12:04, 25 October 2023 Pascale talk contribs deleted page Annotation Cross Products (Retired) (content was: "#REDIRECT:Annotation <span style ="color:red">'''Please note, this page no longer contains the primary documenation for the annotation extension field. Information here is being moved to the main Annotation Extension wiki page, and supporting pages.'''</span> <strike>'''NB: Annotation cross-products are now referred to as annotation extensions''' Each GO annotation pairs a si...", and the only contributor was "Cjm" (talk))
- 12:03, 25 October 2023 Pascale talk contribs undeleted page Annotation Cross Products (Retired) (155 revisions)
- 07:58, 18 September 2023 Pascale talk contribs deleted page Ontology meeting 2023-09-11 (content was: "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Precompute inferred taxon constraints and add to ontology release= See https://github.com/geneontology/go-ontology/issues/19759 =[https://github.com/geneontology/go-ontology/issues/21211 Odd parent - child relationships for binding MF terms]=...", and the only contributor was "Pascale" (talk))
- 03:38, 13 September 2023 Pascale talk contribs deleted page Category:Protein Complex (content was: "All things protein complex.", and the only contributor was "Gail" (talk))
- 03:40, 12 September 2023 Pascale talk contribs deleted page Creating new GO terms (content was: " Category:OntologyCategory:GO Editors", and the only contributor was "Pascale" (talk))
- 10:40, 13 June 2023 Pascale talk contribs deleted page Small molecule to Molecular Function relations (content was: "== Relations for Small molecule to Molecular Function == {| class="wikitable" !Ontology Pair !Relation !Usage |- |rowspan="4"| Small molecule to Molecular function |has small molecular activator | Links a small molecule (ChEBI) to a Molecular Function or Biological Process the small molecule activates. |- |Has small molecular inhibitor...", and the only contributor was "Pascale" (talk))
- 09:55, 9 June 2023 Pascale talk contribs deleted page Annotation Extension Relation:during (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a process during which a molecular function or biological process occurs or a cellular component is present. ==Child terms== * exists_during * happens_during ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== BF...")
- 08:46, 16 March 2023 Vanaukenk talk contribs deleted page Causally upstream of (We no longer want to use causal relations without directionality.)
- 08:38, 22 February 2023 Pascale talk contribs deleted page Editor Guide to Regulates (content was: "==How to make new terms== <br> When making a new set of regulates terms here are the things you need to know. <br> You make new terms like this:<br> <br> [i] isotropic growth The process being regulated. ---[r] regulation of isotropic growth standard regulation term. ------[pr] positive regulation of isotropic growth standard regulation term. ---------[i] photoreceptor response to blue light The process doing the...")
- 08:35, 22 February 2023 Pascale talk contribs deleted page Regulates Documentation (2007) (content was: "Category:Regulation ==GO Website Documentation== Image:Regulates_documentation.doc")
- 08:35, 22 February 2023 Pascale talk contribs deleted page File:Regulates documentation.doc (Deprecated)
- 08:34, 22 February 2023 Pascale talk contribs deleted page File:Curator regulates documentation.doc (Deprecated)
- 08:10, 22 February 2023 Pascale talk contribs deleted page Binding discussion emails (content was: "Category:Deprecated =GO RULE: [https://github.com/geneontology/go-site/tree/master/metadata/rules#gorule0000007 IPI should not be used with GO:0003824 catalytic activity or descendents]= == Links == 2010_GO_camp_binding_documentation_issues 2010_GO_camp_binding_documentation_issues#Agenda_for_discussion_26-05-2010 == Using column 16 in conjunction with an catalytic activity annotation == Would it be possible to include a further discussion on column 16 in th...")
- 07:42, 22 February 2023 Pascale talk contribs deleted page Enzyme Alignment (content was: "Category:Ontology ==Summary== Align the reaction / catalytic activity terms in GO with those in external databases such as MetaCyc, EC, KEGG, etc.. ==Personnel== Amelia, Chris, David, Jane, Tanya ==Plan of Action== The plan is to create GO terms that correspond to the reactions that enzymes catalyse; rather than follow EC's system, which is gene product-based, and allows an enzyme to catalyse a number of different reactions, follow a system like that of MetaCyc, KEGG r...")
- 06:49, 22 February 2023 Pascale talk contribs deleted page Regulators (content was: "The goal is to clean up existing enzyme/catalytic activity regulator, activator and inhibitor terms in MF: we should only keep those that represent a direct molecular activity that regulates the activity of another gene product. Examples that we would allow include classical competitive inhibition, and probably noncompetitive and uncompetitive inhibition as well (must confirm)....", and the only contributor was "Midori" (talk))
- 06:49, 22 February 2023 Pascale talk contribs deleted page Enzyme binding discussion (content was: "Category:Binding == '''enzyme binding ; GO:0019899 Interacting selectively and non-covalently with any enzyme.''' == <span style=color:GREEN> '''Q1: Can this term be used to annotate binding to ANY subunit of an enzyme complex, or is it restricted to binding to the CATALYTIC SUBUNIT ONLY ?</span>''' Related SF item: https://sourceforge.net/tracker/?func=detail&aid=2983894&group_id=36855&atid=440764 This will also affect the ontology structure, because we have: protei...")
- 09:42, 16 February 2023 Vanaukenk talk contribs deleted page Indirectly causally upstream of (content was: "===Annotation usage=== This relation should not be used for annotation, either in standard annotation extensions or in GO-CAMs. ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.'' === Ontology usage === This relation should not be used in the ontology. == Relations Ontology == [https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012011 indirectly causal...")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Category:Publications (content was: "All GO-related publications from GOC members", and the only contributor was "Cjm" (talk))
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, tutorials, talks, posters (content was: "Publications, Talks, Posters 2018 Publications, Talks, Posters 2017 Publications, Talks, Posters 2016 Publications, Talks, Posters 2015 Publications, Talks, Posters 2014 Publications, Talks, Posters 2013 Publications, Talks, Posters 2010-2012 Publications, Talks, Posters 2007-2009 Publications, Talks, Posters 2003-2006 Category:Publications")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2018 (content was: "Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea AZ, Acquaah V, Martin MJ, Mayr M, Lovering RC. (2018 Advance publication) [http://rnajournal.cshlp.org/content/early/2018/06/05/rna.065565.118.abstract Expanding the horizons of microRNA bioinformatics]. RNA. Jun 5. doi: 10.1261/rna.065565.118. Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Ri...")
- 12:30, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2017 (content was: "Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 6:10. https://doi.org/10.1186/s13630-017-0054-8 Category:Archived")
- 12:28, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2016 (content was: "Category:Archived ==List of papers published by GOC in 2016== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Hill DP, D'Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology. Database (Oxford). 2016 Sep 1. PMID 27589964. * Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gille...")
- 12:26, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2015 (content was: "Category:Publications ==List of papers published by GOC in 2015== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Eme...")
- 12:23, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2014 (content was: "Category:Archived ==List of Papers published by GOC in 2014 (Chronologically, most recent first)== * Ascensao JA, Dolan ME, Hill, DP and Blake JA. 2014. Methodology for the inference of gene function from phenotype data. <i>BMC Bioinformatics</i>. 15:405 doi:10.1186/s12859-014-0405-z. * The Gene Ontology Consortium. 2014. Gene Ontology Consortium: Going Forward. ''Nucl. Acids Res.'' Database Issue doi: 10.1093/nar/gku1179. * Dietze H, Berardini TZ, Foulger RE, Hill DP,...")
- 12:18, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2013 (content was: "Category:Archived == Journal Publications == Blake JA . 2013 Ten Quick Tips for Using the Gene Ontology. PLoS Comput Biol 9(11): e1003343. doi:10.1371/journal.pcbi.1003343. Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, & Wilkinson MD. 2013. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of biomedical semantics, 4(1), 2. [http://www.ncbi.nlm.nih.gov/pubmed/23286517 PMID:23286517] Assel...")
- 12:16, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2012 (content was: "Note there is now a GO group on Mendeley: http://www.mendeley.com/groups/1250271/gene-ontology-consortium/papers/ Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2010 reporting year. === Publications (alphabetical) === * Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2012 Dec 16. doi: 10....")
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010- (content was: "#REDIRECT Publications, Talks, Posters 2010-2011", and the only contributor was "Jl242" (talk))
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2011 (content was: "#REDIRECT Publications, Talks, Posters 2010-2012", and the only contributor was "Cjm" (talk))
- 11:56, 10 February 2023 Pascale talk contribs deleted page GO publications 2009 (content was: "Category:Publications Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2009 reporting year. === 2009 Publications === #Alterovitz, G., Xiang, M., Hill, D., Lomax, J., Liu, J., Mungall, C., Harris, M., Dolan, M.E., Blake, J.A., Ramoni, M.F. Engineering Biomedical Ontologies: The Gene Ontology [Accepted, In Press, Nature Biotechnology] #Barrell D., Dimmer E., Huntley R.P., Binns D., O'...")
- 11:43, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2007-2009 (content was: "'''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2007 – 2009''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2009== GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources ==2008== ===2008 Publications === Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gann...")
- 11:39, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2003-2006 (content was: "=Moved to [https://docs.google.com/document/d/1w8nR5llrexyqCKk3NTlj3v3s7gKBA-DPtAT3LiIe5jo/edit#heading=h.ol811igyzk6h Google drive]= '''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2003 – 2006''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2006== ===2006 Publications === Rubin, D.L., Lewis, S.E., M...")
- 10:59, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:57, 10 February 2023 Pascale talk contribs deleted page Category:Metrics (content was: "Pages describing metrics for ontology development", and the only contributor was "Midori" (talk))
- 10:56, 10 February 2023 Pascale talk contribs deleted page Taxon Trigger File Metrics (content was: "For more details see Taxon_Main_Page. This is a list of the stages that we need to complete in the implementation of the taxon trigger file for the project to be considered complete. Where blockages have been hit, these are noted. ===In order:=== * Figure out the theory - '''Done''' * Agree the theory with the GO Consortium - '''Done''' * Agree the theory of Union_of terms with Consortium - '''Not Done''' * Set up the files in scratch and make filtering perl scripts - '...")
- 10:53, 10 February 2023 Pascale talk contribs deleted page Category:Timelines (content was: "Timelines associated with various projects in GO.", and the only contributor was "Gail" (talk))
- 10:51, 10 February 2023 Pascale talk contribs deleted page Cross Product Timeline (content was: "Category:Archived * See also Cross Product Guide == Blessing of mature XP files == Mature xps currently live in scratch dir: cvs/go/scratch/xps biological_process_xp_cellular_component.obo biological_process_xp_cell.obo cvs/go/scratch/regulates_xp_live We will officially bless these and move them out of scratch into go/ontology/editors/xps/ This will happen after the RO meeting ('''May 2008''') Note these will still be external to the main GO file....")
- 10:47, 10 February 2023 Pascale talk contribs deleted page OBO-Edit Release Timeline (content was: "Category:Archived The OBO-Edit calendar tracks releases and working group meeting dates. It's on google and open to the public domain. *[http://www.google.com/calendar/embed?src=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ View the OBO-Edit calendar] = Projected Dates = Refer calendar - If the projected dates are not in the future the calendar has not been able to refresh - access web google calendar externally. [http://wiki.geneontology.org/i...")
- 10:47, 10 February 2023 Pascale talk contribs deleted page Category:To be reviewed (content was: "Pages that David, Kimberly and Pascale have identified as needing review.", and the only contributor was "Pascale" (talk))
- 10:41, 10 February 2023 Pascale talk contribs deleted page Tracker wishlist (content was: "Category:Archived ==Requirements for a GO wiki/tracker system== ===Our high priorities:=== *General **Calendar / time lines / to do lists to show what curators have planned **Create personal pages which show what someone is working on *Tracker **Add user configurable categories to an entry, e.g. how easy it is to complete, whether it would need people to look at annotations, which interest groups it may affect **Be able to configure the order of comments, perhaps with a hy...")
- 10:39, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:09, 10 February 2023 Pascale talk contribs deleted page Category:Logos (content was: "Miscellaneous logos. Category exists to make it easy to find logos that have already been uploaded to this site. However, most logos that have been uploaded were uploaded before this category was created.", and the only contributor was "Clements" (talk))
- 10:03, 10 February 2023 Pascale talk contribs deleted page Browse help page (content was: "<h2>Browsing the Ontology</h2> <p> In AmiGO, the ontology is presented as a tree of terms. An example of part of a tree is displayed below: </p> <br> Image:Organelle.jpg <br> <p> The level of a term is represented by its indentation within the tree, with general terms being less indented than more specific terms. In the above image, you can see that "extracellular organelle" is a child (less specific) term of "organelle", and a sibling term of "intracellular organelle". Eac...")
- 10:00, 10 February 2023 Pascale talk contribs deleted page Regular Expressions accepted by UniProt for use in the 'with' field (content was: "Category:Archived =This information is now in https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml= { prefix => 'UniProt(?:KB)?', id => '[A-Z][0-9][A-Z0-9]{3}[0-9]((-([0-9]+)|:PRO_[0-9]{10}))?' }, { prefix => 'CGD', id => '(CAL|CAF)[0-9]{7}' }, { prefix => 'SGD', id => 'S[0-9]{9}' }, { prefix => 'dictyBase', id => 'DDB_G[0-9]{7}' }, { prefix => 'FB', id => 'FBgn[0-9]{7}' }, { prefix => 'GeneDB_Spombe|PomBase', id =>...")
- 09:58, 10 February 2023 Pascale talk contribs deleted page Category:ZFIN (content was: "#REDIRECT Category:Reports:ZFIN", and the only contributor was "Pascale" (talk))
- 09:57, 10 February 2023 Pascale talk contribs deleted page Category:WormBase (content was: "#REDIRECT Category:Reports:WormBase", and the only contributor was "Pascale" (talk))