Does Logos have a Software Development Position on OS deep linking?

In the last six months I have been developing a 'second brain' or personal knowledge management system on Obsidian for the Mac.

I have come to the point where I need to work out how Logos fits into my workflows. (I already have done this with Obsidian and DevonThink)

The brilliance of Obsidian and DevonThink is that I can use deep links to connect notes and archives together.

As I have tried to do this with Logos, I have not found any capabilities that would enable this. The excellent Hookmark app does not detect anything when I am in a Logos note. I am also unable to put a valid link from another app into a Logos note.

Unless I am missing something, I wondered if Logos Developers might consider adding this to a future version of Logos for desktop? The ability to connect to other sources is invaluable for research.

There is a manifesto for this among some software developers and I hope it catches on as it brings a lot of opportunities for digitally joined up thinking between various research and knowledge management software applications.

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Comments

Tony Walker

I understand what you are thinking I think… I have never used obsidian but there are some podcasts that mentioned about GTD and organizing. I am in between using Reminders and Things and decided how I want to use one or both apps for specific purposes.

In just about every window I have seen, if you click on the three vertical dots and near the bottom of the menu it says copy location as. if you click on one of those links will that do what you are wanting?

Donovan R. Palmer

https://community.logos.com/discussion/comment/1245162#Comment_1245162

Hi Tony --

Well done! That is part of the answer. I can be in a note and click 'L4' and it gives me a link. If I am writing in my markdown editor (a.k.a Obsidian) I can take the Logos link and put in to this format:

[A Link To A Great Logos Note](logos4:NotesTool;EditNoteId=8f6c6c565f3d4b3abdeb97878f4ebfee;IsEditorFullSize=false;IsSidebarExpanded=false;IsTrashExpanded=false;SelectedNotebookId=05c69179a1a84526b01a1bf8ec3dc7a5;ShowFullAnchorText=true;Sort=placement;ViewMode=full)

Which then in the Obsidian viewer appears as:

So this is a partial and well received answer!

There are two downsides with this.

1. It is a manual process as opposed to using hookmark app or logos rendering a link that I can just copy and paste. This is a bit of friction to go manual, but hey it works!

2. I still have not found a way to link from another app into a Logos note. The Logos editor does not recognise the link properly.

For researchers, being able to use deep links between digital tools is very useful. Particularly in systems that have proprietary file formats. I hope that in the future Logos developers can keep this as part of their philosophy. They already have some of the functionality, which is outstanding.

On a separate note, over the years I have been reluctant to put everything in Logos. Technology comes and goes, so future proofing my research has always been a priority. I have friends who have thousands of notes in Evernote and it is very hard to get their life's work out now. To that end, I have done most of my base research in RTF and more recently Markdown. With the latter, I can easily move and utilise it with many tools.

I understand this is not always ideal as there are tradeoffs. A compromise is deep linking and I think that is why apps like Hookmark have been so well received by the PKM, BASB and GTD communities.

Thanks again!

P.S. - It is outside of the scope of this forum, but after using Omnifocus, Todoist, Todo, I went with Reminders. I use the 'front end' GoodTask to get some more functionality, though with the recent updates to Reminders, it has level the playing field a bit.

I went 'Reminders Based' because I wanted something that was tightly baked into OSX. Goodtask hit the sweet spot of giving me more features over Reminders alone. I can open my week view in BusyCal and see the flow of tasks due each day against my calendars. Tasks also appear in agenda app for my time based notes. Location based reminders, share sheet and Siri work great.

Tony Walker

https://community.logos.com/discussion/comment/1245170#Comment_1245170

for 1. did you see the shortcut on that menu? you can use option + command + c to copy the link. I assume that it will use the format (html, logos4, etc) that you had previously selected? so no matter what window you are in, you can use that shortcut without having to click the three dots. so at least that one shortcut will put the 'deep link' into your clipboard.

I would have thought the little link icon in the notes feature would take a things:// link but you are right, it doesn't work. that would be useful for some people so maybe they can add it in the future.

I have never heard of the hookmark app. I will check that out. in my 8th year of full-time ministry. youth pastor. married, four kids, mdiv student at the moment. stressed beyond measure. called a relative of a seminary ceo I knew and asked him to help me. he made the comment about gtd not being a spiritual book, but it helped him more than anything else 'secular' in his ministry. read it. tried to implement good bit of it. spent a week in church office with every single paper from every single drawer piled in the middle of my office. then the next few months refining a digital equivalent. years prior I was known for liking to study but not caring about being organized or keeping track of things. to a fault of mine. now, I have had three people in the last few months ask me to give them some pointers. I don’t say that to boast but to truly thank Jesus for even grace that helped me to move stress around. when im stressed now at least it is not because I can’t remember what I did with something or when such and such event or appointment is.

Donovan R. Palmer

https://community.logos.com/discussion/comment/1245172#Comment_1245172

Thanks! Very helpful. I rechecked them all.

Unless I am mistaken, URL and HTML give links to the Logos web app, not to the local application.

L4 works great, I just have to add a bit of code for it to work in a Markdown document.

Wiki gives a link for the Logos Wiki and RL is to use on a Logos Prayer List, also not to the local application.

The only link that gives a local system deep link is L4... but hey it works! Thank you so much for reminding me of these options. 👍 The big missing piece is being able to link a note back to Logos... but maybe in due course!

P.S. - I use GTD workflows every day and have found them very beneficial in helping me keep track of tasks. If not used well, you can be driven just to get more done. Yet if you have poor workflows, you can be driven but for other reasons in the chaos! The goal is to organise tasks so that you don't have to worry about them, get them out of your mind and be present in the moment.

If you are into GTD, consider Building a Second Brain - Tiago Forte. Again, the goal is to get stuff into systems so that you can focus on what is important and be present with people. The BASB stuff leads you further into Personal Knowledge Management, which is where for me Obsidian comes in with the linking to my work in Logos.

John Williston

https://community.logos.com/discussion/comment/1245175#Comment_1245175

I'd like to chime in and request adding deep linking support for Logos, in particular to work with Hookmark. In considering this, I'd like to suggest y'all take a look at the manifesto for ubiquitous linking for reference. Applications that support deep linking through an application registered/understood URL schema, such as Scrivener, DEVONthink, etc., immediately become far more powerful and more productive for users.

I take notes on all subjects in DEVONthink, for example, but I can link to objects in the file system, documents in other systems including Scrivener for writing, and I'd love to be able to link deeply into at least my notes in Logos if not directly to resources as well. The benefits would be fantastic. Bidirectional linking makes it so easy to move back and forth when working academically it's a wonderful addition. Thanks in advance.

John Williston

https://community.logos.com/discussion/comment/1245175#Comment_1245175

I have to ask you: how are you getting those L4 format links working? I don't use Obsidian (yet, though I'll have to give it a look), but when I paste them into DEVONthink markdown documents they don't work. It seems they're unrecognized as a valid format or something. I've done exactly what you've mentioned works with Obsidian, so I thought I'd ask and see if there was something else you had to do. Thanks.

NB.Mick

https://community.logos.com/discussion/comment/1245175#Comment_1245175

Unless I am mistaken, URL and HTML give links to the Logos web app, not to the local application.

Not sure about HTML (I never used it as I thought it was for people using HTML to write a page), but the URL links (https://ref.ly.....) do open the Logos Web app, but then will open the Logos or Verbum local desktop app - or give it focus if it's already running - and open the respective link target there. This should work on Windows and Mac desktops of every supported OS level, I can confirm it for Windows 10. This should be working on other local platforms as well, I think.

Great to hear that L4 works great for you.

RL gives a link somewhat looking like those used in Reading Lists (i.e. on topics.logos.com). This as well as wiki is not intended for usage outside the Logos environment.

John Williston

https://community.logos.com/discussion/comment/1247739#Comment_1247739

Hey, thanks for that information! I find the URL option lets me use links in DEVONthink, which is great! It's a little annoying that I have to go through the intermediary step of letting it launch a page in Safari, which then prompts me every time whether I should allow it to open in the Logos software, but at least it gets me there. Yay!

Lyndon Drake

https://community.logos.com/discussion/comment/1247741#Comment_1247741

This has been very helpful. I have been trying it out and the L4 links work in DEVONThink too. They just don't trigger bringing the Logos application to the front. But it definitely works.

The HTML links are more problematic. E.g. if I have Gibson, Canaanite Myths and Legends open and try to link to CTA 4:2:6, the HTML link brings up Wyatt, Religious Texts from Ugarit and shows CTA 4:2:6 there. It's the same text, but in this case it's finding the English translation book not the actual Ugaritic original.

Just by way of contrast, Accordance works well with Hook, producing fairly neat accord:// links that deep jump into the application. But of course I have many more texts in Logos and having some way to deep link into them is much better than nothing, even if it would be a huge help if Hook worked — and if the L4 URL scheme was a bit neater and more compact, as the long and ugly links really do clutter up a Markdown document!

Donovan R. Palmer

https://community.logos.com/discussion/comment/1251485#Comment_1251485

Accordance Bible Software does indeed work very well with deep links and Hookmark. I hope Logos can someday do it as well. I suspect that it would not be hard to bring Logos up to standard as some of the linkage is already there.

Lyndon Drake

https://community.logos.com/discussion/comment/1251489#Comment_1251489

Exactly. The ability to link exists. It just needs surfacing that in a form that Hookmark can find. Ideally, it would also include condensing the L4 links that do get produced as they are so verbose.

As you say, it's not really new functionality, as it looks like the hardest bit is done. It's just refining it and making it visible to MacOS.

NB.Mick

https://community.logos.com/discussion/comment/1251485#Comment_1251485

The HTML links are more problematic. E.g. if I have Gibson, Canaanite Myths and Legends open and try to link to CTA 4:2:6, the HTML link brings up Wyatt, Religious Texts from Ugarit and shows CTA 4:2:6 there. It's the same text, but in this case it's finding the English translation book not the actual Ugaritic original.

This is weird and I don't think I can duplicate on Windows. Your description would be the intended behavior if you had a datatype link and Wyatt prioritized higher than Gibson, but getting those links from the kebab menu, regardless of L4, URL or HTML (noting I would always use URL, the HTML is only for building websites) on Windows always gives resource links.

MJ. Smith

https://community.logos.com/discussion/comment/1251499#Comment_1251499

CTA 4:2:6 is a reference/milestone which will follow the prioritization of books containing that text in your library. The URL from the Context Menu for this reference (Ugaritic) is https://ref.ly/logosref/CTAUgariticTexts.4:2:6-7. The URL for the location of the English translation in the book is taken from the Panel Menu and is https://ref.ly/logosres/canmythslegtrn?ref=CTAUgariticTexts.4%3a2%3a6-7 . The former will take you to the text in any language or resource based on the prioritization; the latter will take you to a specific location in a specific book.

Lyndon Drake

https://community.logos.com/discussion/comment/1251503#Comment_1251503

You're right, it was from the context menu. I hadn't realised that difference was there between the same command on the context menu and on the panel menu.

That also makes clear that the panel URL link and the L4 link are identical in content just different in form (logosres:canmythslegtxt;ref=CTAUgariticTexts.4:2:6).

MJ. Smith

https://community.logos.com/discussion/comment/1251535#Comment_1251535

same command on the context menu and on the panel menu.

Not quite the same command - one is "copy reference" while the other is "copy location as" - similar but different commands. See L/V 10+ Tip of the Day #132 Split books and links - Logos Forums

Lyndon Drake

https://community.logos.com/discussion/comment/1251540#Comment_1251540

Ah cool, thanks for that and for the tip link too

Lyndon Drake

https://community.logos.com/discussion/comment/1251542#Comment_1251542

Although the tip doesn't make clear that Logos will take a reference link and jump to a *completely different* text, not just one of the three parts of Gibson (in the example I used, a URL link will prefer Gibson, Religious texts from Ugarit, 2nd edition which I happen to have in my library)

MJ. Smith

https://community.logos.com/discussion/comment/1251543#Comment_1251543

This URL does not specify the book to be used so your priority list controls what will actually open.

was intended to indicate that the book was not defined, only the reference. I have clarified the text to read

This URL does not specify the book to be used so your priority list controls what will actually open. The highest priority book containing the milestone for the reference will open.

Donovan R. Palmer

https://community.logos.com/discussion/comment/1247731#Comment_1247731

I have to ask you: how are you getting those L4 format links working? I don't use Obsidian (yet, though I'll have to give it a look), but when I paste them into DEVONthink markdown documents they don't work. It seems they're unrecognized as a valid format or something. I've done exactly what you've mentioned works with Obsidian, so I thought I'd ask and see if there was something else you had to do. Thanks.

You have to manually copy and paste an L4 formatted link to markdown. e.g.

logosres:esv;ref=BibleESV.Ac2.36

[Acts 2:36](logosres:esv;ref=BibleESV.Ac2.36)

the format is:

[hyperlink text](system link)

In markdown the link is then rendered:

NB.Mick

https://community.logos.com/discussion/comment/1251543#Comment_1251543

Logos will take a reference link and jump to a *completely different* text

That's the idea of reference / datatype links. They typically exist when there are multiple resources that contain text that is referenced in the same way (and yes, a bible reference can be thought of as an example of that). That kind of link is extremely helpful when there are multiple editions of the same work (like Calvin's Institutes or Augustin's Confessions) - the link will work for any of them that is indexed according to the respective datatype. Users who own different editions can benefit from the link - as opposed to a resource link that always references the exact same book. Those who own multiple editions (such as different translations, or different languages) can choose which one opens by use of prioritization (it would really be nice if the library had a column with index data to facilitate this a bit more smoothly).

Tes

https://community.logos.com/discussion/comment/1251557#Comment_1251557

Could you please performe it step by step ,so I can follow and make it usable for me as well.

Chas

https://community.logos.com/discussion/comment/1251553#Comment_1251553

Thanks for this, Donovan (and others). As a new and enthusiastic user of DEVONthink and an old timer with Logos, I was pleasantly surprised. I did note, however, that the Logos desktop app needs to be running for the link from DEVONthink to work. If Logos is not running, clicking on the link from within a DEVONthink markdown document will indeed open Logos, but it doesn't go to the desired location. Instead, I get a blank screen.

But I can live with that while we're all waiting for the devs at Logos to add interlinking or contextual computing or whatever it's called. Once you start using this feature to bounce back and forth between apps, it's very hard to go back.

FWIW, all my tests are being run on a MacBook Pro with an M1 processor.

NichtnurBibelleser

https://community.logos.com/discussion/comment/1245175#Comment_1245175

P.S. - I use GTD workflows every day and have found them very beneficial in helping me keep track of tasks. If not used well, you can be driven just to get more done. Yet if you have poor workflows, you can be driven but for other reasons in the chaos! The goal is to organise tasks so that you don't have to worry about them, get them out of your mind and be present in the moment.

I try to follow GTD, too. Would you mind to elaborate a bit on the highlighted parts of the post?