User talk:Julialturner

RELN
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2ddu, 2e26, 2DDU, 2E26, 3A7Q
Identifiers
Aliases	RELN, LIS2, PRO1598, RL, reelin, ETL7
External IDs	OMIM: 600514; MGI: 103022; HomoloGene: 3699; GeneCards: RELN; OMA:RELN - orthologs
Gene location (Human) Chr. Chromosome 7 (human) Band 7q22.1 Start 103,471,381 bp End 103,989,658 bp
Gene location (Mouse) Chr. Chromosome 5 (mouse) Band 5 A3|5 9.98 cM Start 22,089,452 bp End 22,549,700 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in olfactory bulb cerebellar vermis cerebellar hemisphere paraflocculus of cerebellum right hemisphere of cerebellum spinal ganglia trigeminal ganglion endothelial cell tibial nerve Pons Top expressed in ciliary body cerebellar vermis lobe of cerebellum iris olfactory bulb sciatic nerve endothelial cell of lymphatic vessel superior colliculus paraventricular nucleus of hypothalamus piriform cortex More reference expression data BioGPS More reference expression data
Gene ontology Molecular function metal ion binding peptidase activity hydrolase activity serine-type peptidase activity lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding Cellular component cytoplasm dendrite plasma membrane extracellular region extracellular space membrane extracellular matrix neuron projection Biological process NMDA glutamate receptor clustering positive regulation of lateral motor column neuron migration dendrite development proteolysis cerebral cortex development lateral motor column neuron migration positive regulation of phosphatidylinositol 3-kinase signaling positive regulation of TOR signaling long-term memory multicellular organism development receptor localization to synapse postsynaptic density protein 95 clustering ventral spinal cord development protein localization to synapse forebrain development long-term potentiation regulation of gene expression layer formation in cerebral cortex cell migration learning associative learning cell adhesion hippocampus development spinal cord patterning cerebral cortex tangential migration positive regulation of peptidyl-tyrosine phosphorylation glial cell differentiation peptidyl-tyrosine phosphorylation positive regulation of excitatory postsynaptic potential positive regulation of CREB transcription factor activity positive regulation of protein kinase activity modulation of chemical synaptic transmission positive regulation of AMPA receptor activity brain development central nervous system development response to pain positive regulation of synapse maturation positive regulation of long-term synaptic potentiation cell morphogenesis involved in differentiation neuron migration positive regulation of neuron projection development positive regulation of small GTPase mediated signal transduction positive regulation of synaptic transmission, glutamatergic regulation of behavior positive regulation of dendritic spine morphogenesis reelin-mediated signaling pathway regulation of NMDA receptor activity positive regulation of protein tyrosine kinase activity axon guidance Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 5649 19699 Ensembl ENSG00000189056 ENSMUSG00000042453 UniProt P78509 Q60841 RefSeq (mRNA) NM_173054 NM_005045 NM_011261 NM_001310464 RefSeq (protein) NP_005036 NP_774959 NP_001297393 NP_035391 Location (UCSC) Chr 7: 103.47 – 103.99 Mb Chr 5: 22.09 – 22.55 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Infobox gene Module

Is it possible to create parameters name, image and maybe image description in Template:Infobox gene so that it would be possible to edit them? Now this parameters are generated automatically and there is now way to change them. This can become a problem because automatically chosen images are not always the best one. Plus makes this module hard to use in other wikipedias, where names of genes or proteins are not written in English.Эрг (talk) 16:56, 21 May 2016 (UTC)

@Эрг: Hi, yes it is possible to change the image. Under the new infobox_gene you will see links to wikidata. The image under the human gene wikidata item will need to be changed/added to include the desired image link. Is there a particular example you are looking at, so that I could go through step by step to show you how to change it?Julialturner (talk) 19:02, 21 May 2016 (UTC)

@Julialturner: No, thanks. Now that you mentioned wikidata, I got it. But my main problem with this template still stays. You see, I localized your great module for Russian wikipedia and easily translated it, but the template generated keep displaying it's name on English. Is it possible to do so that the template displays it's own name (label) according to the language of wikipedia it is used in, the same way it displays GO ids? Also, as I said before, it would be nice to have an image description parameter. One more time thank you for your hard work, it's really awesome.--Эрг (talk) 21:31, 21 May 2016 (UTC)

@Эрг: I will look into translating the label. Maybe @I9606: will have some input? I am surprised that the GO ids are translated and will try to see what the mechanism that is at work here. Thanks for input in making the module more usable. Julialturner (talk) 21:15, 22 May 2016 (UTC)

@Эрг and Julialturner: Which label are you referring to? Wikidata has a mechanism to adapt its interface display of labels and descriptions based on the locale of the user - this is probably how the GO terms are being adapted. If you mean the label of the template itself??? that label wouldn't be in wikidata hence would not get the same automatic adaptation. On the image front, I think we could probably add the image and image description parameters to allow users to override the defaults coming from wikidata. I think that would be a good idea. The current one image, one item approach is rather limiting. --Benjamin Good (talk) 21:58, 22 May 2016 (UTC)

@Benjamin Good and Julialturner: What I am referring to is the way Gene ontology section works e. g. the gene ontology section will display QID in Russian wiki if the particular wikidata object have empty field "lable" at the top of the page (where the Language field is). So, If you fill this field in it will display correct phrase for given GO id (and each GO id is has it's own wikidata object). My point is why not to make Infobox_gene module to request it's name (the line displayed at the top of the box on the wikipedia page) the same way it does with GO ids? This way, by editing one wikidata object, it will be possible to adjust this template for any given language. The same thing should be done with another multilingual param - image description (if we would have any). I think it snould be possible to use the same piece of code, used for getting GO ids from wikidata, for aforementioned params (even if we don't quite understand how does it work). This, and you should probably white an extensive guide on how to edit this new template through the means of wikidata.--Эрг (talk) 23:03, 26 May 2016 (UTC)

P.S You can see how this works on the page ru:Тиоредоксин, which I experimented with.--Эрг (talk) 23:06, 26 May 2016 (UTC)

need help with zh wiki localization

in Gene ontology section, if the biological role has no chinese name on wikidata, it will display it's QID. Is it possible to make it fallback to english when there's no chinese data?example Panintelize (talk) 03:09, 26 May 2016 (UTC)

@Panitelize: I am not sure let me look into it. Julialturner (talk) 05:21, 26 May 2016 (UTC)

@Panitelize: You can just go to the wikidata page of this item and edit it's lable field, right at the top of the page. Create field for Chinese language and write down an appropriate translation - then it will be displayed correctly on your language. --Эрг (talk) 22:32, 26 May 2016 (UTC)

@Эрг:where can I find a full list of used items?Panintelize (talk) 06:22, 5 June 2016 (UTC)

@Panitelize:Fallback is possible with e.g. mw.wikibase.sitelink(id) or (':en' .. mw.wikibase.getEntity(id):getSitelink('enwiki')) or ('d:' .. id), but according to the document this method generates a costly operation by fetching the whole entity. I have filed T148115 to request non-expansive interwiki sitelink fetching. --Artoria2e5 emits crap 04:01, 14 October 2016 (UTC)

Infobox Gene problem

The article Major histocompatibility complex, class II, DQ alpha 1 has a script error, which looks like it’s happening around your last change to Module:Infobox gene. Could you have a look at it? As far as I can tell nothing is wrong with the article or its data.--JohnBlackburne^words_deeds 03:46, 31 May 2016 (UTC)

@JohnBlackburne: Thank you for making me aware of this scripting error. It has been corrected.Julialturner (talk) 05:44, 31 May 2016 (UTC)

Chromosome category

Hello. Are there any plans to make {{Infobox_gene}} put the articles to corresponding categories based on chromosome they are located on, like Category:Genes on human chromosome 1?--RoadTrain (talk) 01:11, 1 June 2016 (UTC)

@RoadTrain: Sure that is a good idea. I will look into how to get these added. Julialturner (talk)

@Julialturner: First of all, thanks for doing it! Please take a look at what I did in Russian wiki to properly extract chromosome number (trimChromosome) from a wikidata item. It feels more generic, though may not account for all possible errors.--RoadTrain (talk) 13:23, 20 June 2016 (UTC)

@RoadTrain: Thanks for the suggestion. That is a nice way to make to the code more concise. Have you gotten an feedback from others on the russian wikipedia about the categories within the templates. One of my categories was reverted see the notes on this edit.... https://wiki.riteme.site/w/index.php?title=Template%3AInfobox_gene&type=revision&diff=725200450&oldid=722220268 Julialturner (talk) 21:13, 20 June 2016 (UTC)

Haven't gotten any feedback. I think that particular revert was due to Human proteins category having complicated multi-level structure. Chromosome categories, on the other hand, are essentially 1-level, so I think that's alright.--RoadTrain (talk) 21:25, 20 June 2016 (UTC)

@RoadTrain: How does your edit deal with those genes on the X and Y chromosome?

Yes, I've just updated the code to account for those.--RoadTrain (talk) 21:57, 20 June 2016 (UTC)

@RoadTrain: I updated with a combo of old and new, so now checks for data that looks like chromosome as before (which keeps it from generating errors) and then added the more generic extraction. 70.95.134.121 (talk) 05:43, 21 June 2016 (UTC)

moving all displayed text to the top of code(as variables?) for easier localization and update

If the maintainer on other wikis wants to update the code they can just switch out the bottom part --Panintelize (talk) 06:21, 5 June 2016 (UTC)

I support this suggestion. I think all localizeable stuff should be defined in one place.--RoadTrain (talk) 22:08, 5 June 2016 (UTC)

If I understand you correctly, then you like all the code contained in the variable "root" at the top of the code. Is this what you had in mind? Julialturner (talk) 21:42, 6 June 2016 (UTC)

@Julialturner:I am not familiar with the code, I want all the code containing visible part to reader moved to the top, so maintainer in each language can localize more easily. And when there's major update it's easier to push it to multiple wikis(swapping out the bottom part not containing localization) Panintelize (talk) 02:31, 18 July 2016 (UTC)

@Panintelize: Unfortunately, the part of the code that is used to render the box can't easily be moved to the top as it is dependent on the logic within the function it resides. I tried to organize it so 1. It gets data 2. It gets values from Data. 3. Uses values to create html/wiki code.

I have no experience in js so what I am about to suggest might not make any sense. But I'll ask anyway.

Is it possible to define a function at the top of code that returns strings of text to numbers? e.g. f(1)='Available structures' f(22)='Orthologs' f(23)='Species' f(11)='Genetically Related Diseases'. And whenever there's a need to use these text just call the function

is this possible?Panintelize (talk) 05:09, 9 August 2016 (UTC)

@Panintelize:It might be possible, but generally not good practice to use numbers for function names. Let me see if I can modularize it a little more so the list of all values is closer to the top. Julialturner (talk) 19:59, 9 August 2016 (UTC)

also, what do these numbers correspond to? The infobox doesn't always display the same information for different genes, so if you are assuming the numbering is top to bottom, left to right that might get confusing.Julialturner (talk) 21:38, 9 August 2016 (UTC)

Module:Infobox gene problem

I reverted the last change to the Module (by an IP but I assume that is you logged out) as it was generating dozens, maybe a hundred, errors on Gene pages, based on it being the only recent change. See the category, Category:Pages with script errors which I periodically check. The problem pages are still listed as the category takes some time to update, in case you want to see the error, and which pages are having problems in case you want a testcase for e.g. testing a sandbox version.--JohnBlackburne^words_deeds 21:25, 20 June 2016 (UTC)

Yes, it's my fault. I believe I've fixed it.--RoadTrain (talk) 21:55, 20 June 2016 (UTC)

No you broke it again. See e.g. Actin which has (or had) the error:

Lua error in Module:Infobox_gene at line 929: attempt to concatenate local 'chr' (a nil value).

Here’s a list of the pages that were generating errrors before I reverted: Actin, Actinin, ATP synthase, Casein kinase 1, Casein kinase 2, DiGeorge syndrome, Tyrosine aminotransferase. There could be many more: the category takes time to populate, time to empty especially when it’s not the pages but underlying templates and modules that changed. Again, changes to such a highly visible template should really be tested first in its sandbox/with testcases.--JohnBlackburne^words_deeds 22:03, 20 June 2016 (UTC)

@JohnBlackburne:It's not my fault this time. The articles you list don't even have wikidata information for this module, and hence should not have this template in them. I surely can add an extra check for chr not to be nil, but there's little point if the module is used this way.--RoadTrain (talk) 22:10, 20 June 2016 (UTC)

@JohnBlackburne and RoadTrain: I will look into why those pages without wikidata items exist and for the time being the code is reverted. Julialturner (talk) 22:23, 20 June 2016 (UTC)

[1]; Template:PBB/6898; wikidata:Q7861685; wikidata:Q21172675; wikidata:Q18298361 - wrong wikidata item assigned?--RoadTrain (talk) 22:27, 20 June 2016 (UTC)

Looking at Actin the box was added by ProteinBoxBot, so you should take it up with that bot I guess. But it has been added, to that and perhaps dozens or hundreds of pages without data, so it probably should be a test case for it – a page with incomplete or missing data.--JohnBlackburne^words_deeds 22:32, 20 June 2016 (UTC)

Image description

Hello again! Did you think about how we can add localized descriptions for gene's image? It was specifically requested on Russian wiki. Can you please suggest any solutions? Thanks.--RoadTrain (talk) 09:00, 24 June 2016 (UTC)

Maybe we can add an optional parameter to {{Infobox gene}} which will forward it to the module, and will add/replace a default image/description in the infobox?--RoadTrain (talk) 09:28, 24 June 2016 (UTC)

Hi, @RoadTrain: unfortunately at this time I don't have a good way add the image caption as it is not currently in wikidata and will take some restructuring to add to wikidata. It exsits in the wiki commons image description. If you have any ideas on how to access this via a lua module then I could add it. Julialturner (talk) 00:31, 25 June 2016 (UTC)

Infobox gene proposal

Hi Julia. I have made several proposals at Module talk:Infobox_gene (IUPHAR links, EC links, Making Infobox gene more understandable). I would appreciate your feedback. Thanks. Boghog (talk) 08:20, 28 July 2018 (UTC)

@Boghog: Hello. I think your suggestions sound good. I have been out of the loop of what the current plans are for the gene infobox, but would be willing to help if you have any lua related questions. Best Julialturner (talk) 14:02, 31 July 2018 (UTC)

User:ProteinBoxBot blocked

I have blocked User:ProteinBoxBot and started a discussion at Wikipedia:Bots/Noticeboard#User:ProteinBoxBot. Fram (talk) 08:26, 24 October 2018 (UTC)

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