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10.1093/genetics/iyab149 #1776

Open bioentity-bot opened 10 months ago

bioentity-bot commented 10 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyab149

bioentity-bot commented 10 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyab149 @kyook New publication uploaded.

kyook commented 10 months ago

Hi @ValWood and @manulera. I've assigned you to the first Pombe paper. To orient you a bit, the link in the email alert you received should open to the paper view of the article. I've already run the linker, you just need to vet the linked entities as pombe entities that you want linked. The entities linked are underlined in yellow. Everything that is italicized is in red, by default. Please let @nickstiffler know if you need linking rules set and if you would prefer a different color or highlighting format for this link editor. The published GSA paper color all links a non-disruptive dark blue.

In the right column under Links, you should see a list of the entities that were identified based on the pombe gene list I ran on it. If you see a yellow warning sign next to an entity, it means there were a couple matches. The system chooses one, but will present you with all possible matches. just click on the arrow to open the subwidget and you can set the correct match. Example is here: cds1 was recognized as a match for two different potential entities, cds1 and bbl1, the system auto-linked it to bbl. Screenshot 2023-11-03 at 11 15 22

Also, each paper has it's own github ticket you can access the thread for each paper through the Curator's note link see image

Screenshot 2023-11-03 at 11 20 47

ValWood commented 10 months ago

Hi @kyook I think it will be easier if you give me a quick demo. I tried one, but I could not see how to get beyond the abstract. Also it wasn't immediacy obvious how to locate the papers (the links did not appear to be publication specific).

kyook commented 10 months ago

Hi Val, I was away so sorry for the delay. Do you have time tomorrow (Thursday)


Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: ***@***.***
email: ***@***.***
email: ***@***.***
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150

On Sun, Nov 12, 2023 at 3:29 AM Val Wood ***@***.***> wrote:

> Hi @kyook <https://github.com/kyook> I think it will be easier if you
> give me a quick demo. I tried one, but I could not see how to get beyond
> the abstract. Also it wasn't immediacy obvious how to locate the papers
> (the links did not appear to be publication specific).
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/bioentity/papers/issues/1776#issuecomment-1807085076>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAEVKGWGLSOUD3AC4EIWCULYECQJLAVCNFSM6AAAAAA6RUEFAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGA4DKMBXGY>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
kyook commented 10 months ago

We can meet you tomorrow at 8:30am pacific, 4:30 your time Val?


Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: ***@***.***
email: ***@***.***
email: ***@***.***
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150

On Wed, Nov 15, 2023 at 12:47 PM Karen Yook ***@***.***> wrote:

> Hi Val, I was away so sorry for the delay.  Do you have time tomorrow
> (Thursday)
> ~~~~
> Karen Yook
>
> Curator / Editor
> WormBase Caltech / microPublication
> email: ***@***.***
> email: ***@***.***
> email: ***@***.***
> skype name: wbkaren
> zoom channel: https://caltech.zoom.us/j/5465231995
> tel: +1(415)306-4150
>
>
> On Sun, Nov 12, 2023 at 3:29 AM Val Wood ***@***.***> wrote:
>
>> Hi @kyook <https://github.com/kyook> I think it will be easier if you
>> give me a quick demo. I tried one, but I could not see how to get beyond
>> the abstract. Also it wasn't immediacy obvious how to locate the papers
>> (the links did not appear to be publication specific).
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <https://github.com/bioentity/papers/issues/1776#issuecomment-1807085076>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/AAEVKGWGLSOUD3AC4EIWCULYECQJLAVCNFSM6AAAAAA6RUEFAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGA4DKMBXGY>
>> .
>> You are receiving this because you were mentioned.Message ID:
>> ***@***.***>
>>
>
kyook commented 10 months ago

Hi Karen,

Yes I can do this slot!

Talk tomorrow.

Val

On 15/11/2023 19:49, Karen Yook wrote:

We can meet you tomorrow at 8:30am pacific, 4:30 your time Val?

Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: ***@***.***
email: ***@***.***
email: ***@***.***
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150

On Wed, Nov 15, 2023 at 12:47 PM Karen Yook ***@***.***> wrote:

    Hi Val, I was away so sorry for the delay.  Do you have time
    tomorrow (Thursday)
Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: ***@***.***
email: ***@***.***
email: ***@***.***
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150

On Sun, Nov 12, 2023 at 3:29 AM Val Wood
***@***.***> wrote:

    Hi @kyook
    <https://github.com/kyook>
    I think it will be easier if you give me a quick demo. I tried
    one, but I could not see how to get beyond the abstract. Also
    it wasn't immediacy obvious how to locate the papers (the
    links did not appear to be publication specific).

    —
    Reply to this email directly, view it on GitHub
    <https://github.com/bioentity/papers/issues/1776#issuecomment-1807085076>,
    or unsubscribe
    <https://github.com/notifications/unsubscribe-auth/AAEVKGWGLSOUD3AC4EIWCULYECQJLAVCNFSM6AAAAAA6RUEFAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGA4DKMBXGY>.
    You are receiving this because you were mentioned.Message ID:
    ***@***.***>

--------------6bV0kaXJ9a1Cr4NGoOFAJvFb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit



Hi Karen,

Yes I can do this slot!

Talk tomorrow.

Val


On 15/11/2023 19:49, Karen Yook wrote:
We can meet you tomorrow at 8:30am pacific, 4:30 your time Val?
~~~~
Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email:
email:
email:
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150


On Wed, Nov 15, 2023 at 12:47 PM Karen Yook <> wrote:

On Sun, Nov 12, 2023 at 3:29 AM Val Wood <> wrote:

Hi I think it will be easier if you give me a quick demo. I tried one, but I could not see how to get beyond the abstract. Also it wasn't immediacy obvious how to locate the papers (the links did not appear to be publication specific).

—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you were mentioned.Message ID: <bioentity/papers/issues/1776/1807085076@github.com>


--------------6bV0kaXJ9a1Cr4NGoOFAJvFb--

kyook commented 10 months ago

Ok, see you then. https://caltech.zoom.us/j/97679833109?pwd=aEVINTB5SDIxeXlocjdid25OeU9LQT09


Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: ***@***.***
email: ***@***.***
email: ***@***.***
skype name: wbkaren
zoom channel: https://caltech.zoom.us/j/5465231995
tel: +1(415)306-4150

On Wed, Nov 15, 2023 at 1:40 PM Valerie Wood ***@***.***> wrote:

>
>
> Hi Karen,
>
> Yes I can do this slot!
>
> Talk tomorrow.
>
> Val
>
>
> On 15/11/2023 19:49, Karen Yook wrote:
>
> We can meet you tomorrow at 8:30am pacific, 4:30 your time Val?
> ~~~~
> Karen Yook
>
> Curator / Editor
> WormBase Caltech / microPublication
> email: ***@***.***
> email: ***@***.***
> email: ***@***.***
> skype name: wbkaren
> zoom channel: https://caltech.zoom.us/j/5465231995
> tel: +1(415)306-4150
>
>
> On Wed, Nov 15, 2023 at 12:47 PM Karen Yook ***@***.***> wrote:
>
>> Hi Val, I was away so sorry for the delay.  Do you have time tomorrow
>> (Thursday)
>> ~~~~
>> Karen Yook
>>
>> Curator / Editor
>> WormBase Caltech / microPublication
>> email: ***@***.***
>> email: ***@***.***
>> email: ***@***.***
>> skype name: wbkaren
>> zoom channel: https://caltech.zoom.us/j/5465231995
>> tel: +1(415)306-4150
>>
>>
>> On Sun, Nov 12, 2023 at 3:29 AM Val Wood ***@***.***>
>> wrote:
>>
>>> Hi @kyook <https://github.com/kyook> I think it will be easier if you
>>> give me a quick demo. I tried one, but I could not see how to get beyond
>>> the abstract. Also it wasn't immediacy obvious how to locate the papers
>>> (the links did not appear to be publication specific).
>>>
>>> —
>>> Reply to this email directly, view it on GitHub
>>> <https://github.com/bioentity/papers/issues/1776#issuecomment-1807085076>,
>>> or unsubscribe
>>> <https://github.com/notifications/unsubscribe-auth/AAEVKGWGLSOUD3AC4EIWCULYECQJLAVCNFSM6AAAAAA6RUEFAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBXGA4DKMBXGY>
>>> .
>>> You are receiving this because you were mentioned.Message ID:
>>> ***@***.***>
>>>
>>
>
kyook commented 10 months ago

Re-ran linking with Pombe_gene, case insensitive ON

ValWood commented 9 months ago

Hi,

In this session the linker appears to be working only on protein names, but not on italicized gene names. Could you check why italicized names aren't linking before I continue?

Thanks

Val

kyook commented 9 months ago

Hi Val, it looks like the italicized gene names were linked, and were annotated with yellow underlines, only the entity itself is still in red like all other italicized words, so they may not look like they were linked. I asked @nickstiffler to take a look to see if he could adjust the colors.

ValWood commented 9 months ago

Hi,

Oddly most of them are now linked. Last night I am sure that the italicized names weren't linked. Maybe I'm mistaken.

However, the systematic names are still not linked: see below:

Screenshot 2023-11-28 at 07 08 05
ValWood commented 9 months ago

Note that SPCC663.08 should be SPCC663.08c, but the other 2 are correct systematic IDs