Chinmay26

Welcome to Wikidata, Chinmay26!

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If you have any questions, don't hesitate to ask on Project chat. If you want to try out editing, you can use the sandbox to try. Once again, welcome, and I hope you quickly feel comfortable here, and become an active editor for Wikidata.

Best regards! Ricordisamoa 21:09, 16 April 2013 (UTC)

April 2013

Hello, I'm Ricordisamoa. I wanted to let you know that I undid one or more of your recent contributions because it didn't appear constructive. Feel free to use the sandbox for test edits. If you think I made a mistake, or if you have any questions, you can leave me a message on my talk page. Thanks! --Ricordisamoa 21:09, 16 April 2013 (UTC)

I will avoid these mistakes in the future. I was trying to get familiar with wikidata statements, properties etc. I will be using Wikidata Sandbox in the future. Chinmay26 (talk) 09:13, 18 June 2013 (UTC)

GSoC

Hi Chinmay! Thanks for the message. Which properties are needed for GSoC? Property creation would go faster if more people would vote from the GeneWiki Project. I need at least two positive votes to create a property and that is already a very low number. (watching your talk page) --Tobias1984 (talk) 09:15, 18 June 2013 (UTC)

Hi Tobias, the proposed set(RNA ID,GenLoc_start,GenLoc_chr,GenLoc_end,GeneAtlasImage,PDB ID) form an integral part of our infobox[[1]]. The other fields have been created.I will reach out to other members of our organisation for support. Chinmay26 (talk) 09:30, 18 June 2013 (UTC)

RefSeq protein ID (P637) is done. --Tobias1984 (talk) 09:20, 18 June 2013 (UTC)

Thanks a lot. But i think the property name should ony be Protein ID.Chinmay26 (talk) 09:32, 18 June 2013 (UTC)

You can change the name. After the property is created it is pretty much up to the users to decide what it should be called. I can only create GenLoc chr, start, end as a string currently. The datatype number is not available yet. We might be able to convert it once the datatype becomes available. How does that sound? --Tobias1984 (talk) 09:42, 18 June 2013 (UTC)

Yes. That's fine. We will incorporate other implemented features as they become availaible. We are also waiting for URL/URI datatypeChinmay26 (talk) 09:56, 18 June 2013 (UTC)

PDB structure ID (P638) is done. --Tobias1984 (talk) 09:42, 18 June 2013 (UTC)

RefSeq RNA ID (P639) is done. --Tobias1984 (talk) 09:46, 18 June 2013 (UTC)

Thanks for creating these set of properties.Chinmay26 (talk) 09:56, 18 June 2013 (UTC)

For the remaining few properties(GeneAtlasImage,GenLoc_chr,GenLoc_start,GenLoc_end), should i reach out to other members for support? Chinmay26 (talk) 10:09, 18 June 2013 (UTC)

I put a message in the project chat. I'm sure we will have a couple more votes within the hour. What about GenLoc_db? I saw you didn't request that one. --Tobias1984 (talk) 10:13, 18 June 2013 (UTC)

We don't want a separate property for GenLoc_db.We plan to have GenLoc_db as a qualifier for the three properties(GenLoc_start ,GenLoc_end, GenLoc_chr). Also we plan to have "RefSeq" as qualifier for Protein ID and RNA ID. Can i create qualifiers myself or only a property creator can do so? Chinmay26 (talk) 10:21, 18 June 2013 (UTC)

Properties and qualifiers are actually the same thing. A qualifier is just a property that further defines a property. Doing statements with qualifiers is a little more flexible. For example if you have a property "image of car" then you can only use if for cars and link to car pictures. On the other hand if you have a property called "image" with a qualifier "depicts" then you can use it everywhere and link to everything. E.g. "image = [car.jpg & depicts = outside of car] & [dashboard.jpg & depicts = interior of car]". --Tobias1984 (talk) 10:33, 18 June 2013 (UTC)

I had one more query. How to establish a link from gene item to webpage. Ex: For reelin [[2]], when we create Entrez Gene ID and fill it with correct value, it automatically takes me to the corresponding NCBI database for reelin. Why does that not happen for Ensembl ID?.How to establish this mapping? --Chinmay26 (talk) 10:29, 18 June 2013 (UTC)

You can request links at MediaWiki talk:Gadget-AuthorityControl.js --Tobias1984 (talk) 10:33, 18 June 2013 (UTC)

Thanks Tobias. Yes,Qualifiers futher refine the meaning of a property. So to create qualifiers, we again have to follow the property proposal procedure?. We want to create the following qualifiers --

• "RefSeq" for Protein ID, RNA ID.
• "GenLoc_db" for GenLoc_start , GenLoc_end , GenLoc_db. Having a window of again 7 days will be further time consuming. Is there a way around this? --Chinmay26 (talk) 11:58, 18 June 2013 (UTC)

I will try to explain the speedy creation on the administrator notice board. But please fill in the template on the property proposal page. --Tobias1984 (talk) 14:31, 18 June 2013 (UTC)

And of course two votes from other users should remain the lower boundary, but if you get all the GSoC participants signed up, that shouldn't be a problem. --Tobias1984 (talk) 14:34, 18 June 2013 (UTC)

It is a little odd that all the messages haven't produced a single vote yet. It's probably a problem that many people don't know what the properties are for and that the Molecular Biology task force might be on summer vacation :). Did you see that I created P643 (P643), genomic start (P644), genomic end (P645). --Tobias1984 (talk) 17:24, 21 June 2013 (UTC)

Thanks for creating those properties!. The reason is that we have decided to move ahead with the current set of well-defined properties. At present, we are going to focus on the Human part of the infobox. We would then incorporate more information of the infobox by proposing the other properties in incremental stages. --Chinmay26 (talk) 17:38, 21 June 2013 (UTC)

RefSeq (P656) is done. The other property got a comment whether the datatype item would be more appropriate. Can you still answer that? --Tobias1984 (talk) 09:59, 22 June 2013 (UTC)

Important molecular biology task force discussions

Hello, you signed up as a participant for the Molecular biology task force. As promised, we are keeping you up to date on important discussions as they arise. Currently, we are very interested in your thoughts on how orthologs are handled in Wikidata. Please chime in here if you have thoughts. There is also another discussion on whether genes and proteins should be combined in a single wikidata item or kept separate. Both these issues are critical for how we model genetic data, and it would be much better if we established solid community consensus now. Your input is appreciated! (Yes, I know you are following the discussions carefully. But in the interest of posting on all participants' talk page, I'm still posting it here...) Cheers, Andrew Su (talk) 00:20, 23 June 2013 (UTC)

genomic assembly (P659)

The property genomic assembly (P659) that you proposed is available now. --Tobias1984 (talk) 12:20, 2 July 2013 (UTC)

Thanks! Is there any problem with "Gene_Atlas image" property which is proposed? --13:05, 2 July 2013 (UTC)

Nothing wrong with the proposal. It just needs more votes. Also there are discussions to only have one image-property and do everything else with qualifiers. So it would be for Reelin "image = PBB_GE_RELN_205923_at_tn.png" & "depicts (qualifier) = Gene Atlas Image". We might need to RfC this topic. --Tobias1984 (talk) 14:41, 2 July 2013 (UTC)

Property proposals

I commented on your proposals: Wikidata:Property_proposal/Term#has_molecular_function. cheers. --Tobias1984 (talk) 12:56, 3 July 2013 (UTC)

molecular function (P680)

The property molecular function (P680) that you proposed is available now. --Tobias1984 (talk) 08:48, 9 July 2013 (UTC)

cell component (P681)

The property cell component (P681) that you proposed is available now. --Tobias1984 (talk) 08:58, 9 July 2013 (UTC)

biological process (P682)

The property biological process (P682) that you proposed is available now. --Tobias1984 (talk) 09:04, 9 July 2013 (UTC)

RfP Bot

Hi Chinmay! Don't forget to get the permission for your bot at Wikidata:Requests_for_permissions/Bot. You could already create the template and add your test edits once the bot is running. I'm already curious to see how things will work out :). --Tobias1984 (talk) 15:19, 9 July 2013 (UTC)

Ok. I plan to finish some work in the next couple of days. I will be applying for bot permissions shortly. Chinmay26 (talk) 15:52, 9 July 2013 (UTC)

ortholog (P684)

The property ortholog (P684) that you supported is available now. --Tobias1984 (talk) 09:34, 10 July 2013 (UTC)

NCBI taxonomy ID (P685)

The property NCBI taxonomy ID (P685) that you supported is available now. --Tobias1984 (talk) 09:58, 10 July 2013 (UTC)

Gene Ontology ID (P686)

The property Gene Ontology ID (P686) that you supported is available now. --Tobias1984 (talk) 14:15, 11 July 2013 (UTC)

encodes (P688)

The property encodes (P688) that you supported is available now. --Tobias1984 (talk) 10:48, 12 July 2013 (UTC)

Remaining properties needed for GSoC project?

Hi Chinmay, are there additional properties needed for your GSoC project? Emw (talk) 03:24, 17 July 2013 (UTC)

The current set of properties covers all aspects. I have proposed one property for each field of PBB templates. . But then we may have a need to further classify them like Ensembl Gene Id and Ensemb protein ID? . Modelling gene info seems a very difficult task!! Chinmay26 (talk) 03:37, 19 July 2013 (UTC)

Agreed! Emw (talk) 10:03, 21 July 2013 (UTC)

Gene Atlas image (P692)

The property Gene Atlas image (P692) that you proposed is available now. --Tobias1984 (talk) 08:41, 17 July 2013 (UTC)

Redundant item for reelin human protein

Hi, I notice you created reelin (Q13561329), which seems to be redundant with reelin (Q13569356). To my understanding the latter is the reference, since it's got site links and has been the one discussed at WT:MBTF. However, I wanted to check with you before nominating Q13561329 for deletion at WD:RFD. Is it OK to delete that item, or are you using it for something? Emw (talk) 12:23, 21 July 2013 (UTC)

Hi, the item corresponds to human gene item for reelin. I need it test modelling purposes.--chinmay

Ah, that makes sense. I've added some notes to the ProteinBoxBot flag request (diff). Cheers, Emw (talk) 13:39, 21 July 2013 (UTC)

encoded by (P702)

Hi, the property encoded by (P702) that you supported in now available. --Paperoastro (talk) 12:48, 21 July 2013 (UTC)

reelin and RELN

Hi Chinmay! Can you take a look at:

• reelin (Q13561329) human protein (for ProteinBoxBot development)
• reelin (Q13569356) human protein
• RELN (Q414043) human gene
• Reelin (Q14155909) -
• Reelin (Q14331165) mouse protein
• Reln (Q13567973) mouse gene
• Reln (Q14331135)

Can any of those items be merged? It looks like we have protein for humans and mice twice. --Tobias1984 (talk) 11:02, 26 August 2013 (UTC)

• reelin (Q13561329) This is the item i use as a sample item for testing and I need it.
• Reelin (Q14155909) Was created by user-emw.
• Reln (Q14331135) This item is mouse reelin protein created by PBB bot. The bot searches for existing items by wikidata-label. When label matches, it checks whether some claims exist in the item. For Protein, claim= uniprot id. If u notice Reelin (Q14155909) did not have uniprot id. So the bot went ahead and created a new item and corresponding uniprot claim in Reln (Q14331135).

I will be utilizing * Reelin (Q14155909) by modifying its claims,label so that there is no duplication. Thanks for pointing this out. Chinmay26 (talk) 11:41, 26 August 2013 (UTC)

Great. Can I ask when your bot will do the first big run? --Tobias1984 (talk) 12:37, 26 August 2013 (UTC)

I am confident it will be up in the next 2-3 days. I have hosted the bot on a server. All that is left is finalizing the test runs,cron jobs. Chinmay26 (talk) 07:10, 27 August 2013 (UTC)

Sounds great. It will be exciting to see the results. --Tobias1984 (talk) 17:39, 28 August 2013 (UTC)

ProteinBoxBot

I've blocked it for having added dozens of duplicate claims. Have you fixed this change? --Ricordisamoa 11:08, 12 September 2013 (UTC)

Yes, I have fixed it. I am handling all items/properties through capitalised id's. The duplicate claims added were because of yesterday.If you notice today's runs https://www.wikidata.org/w/index.php?title=Special:Contributions/ProteinBoxBot&offset=&limit=500&target=ProteinBoxBot, i have fixed them. Currently, I have scheduled a run for 300 genes. Kindly verify it and request you to unblock the bot flag. Thanks Chinmay26 (talk) 11:16, 12 September 2013 (UTC)

 unblocked, sorry. --Ricordisamoa 11:20, 12 September 2013 (UTC)

Thanks.Chinmay26 (talk) 11:23, 12 September 2013 (UTC)

chromosome (P1057)

The property chromosome (P1057) that you supported is available now. --Tobias1984 (talk) 23:18, 24 December 2013 (UTC)

Global Economic Map

Hi Chinmay I have found a lead programmer for the project who is an admin for Wikidata. Thanks for your willingness to get involved but as of now I think only one programmer is necessary. I will let you know if new opportunities arise. Mcnabber091 (talk) 20:43, 9 March 2014 (UTC)

User_talk:ProteinBoxBot#Given_names

Please see the comment above. --- Jura 09:48, 9 May 2015 (UTC)