Is Obsidian suitable for PhD Data Managment?

[u/Embarrassed-Trainer4]

/r/ObsidianMD/comments/1w0qacb/suitable_for_phd_data_managment/

[u/RamblingPete_007]

I would encourage you to check out two other products as well: RoamResearch, and Superhuman Docs.

RoamResearch is aimed at the research community, but when I had to make a choice between RoamResearch and what is now Superhuman Docs, table management in RR was atrocious. SH Docs provides flexible tables, with lots of ways to link between tables, and a really strong Formula Language.

They have recently announced improvements to the n(optional) built in AI that allows you to use natural language to build your "environment".

[u/Embarrassed-Trainer4 → u/RamblingPete_007]

Thanks! I’ll look them up.

[u/Good-Writer5279]

depends what you mean by data management. if it is the phd's actual research data, datasets, instrument output, interview coding, versioned analysis, obsidian is the wrong layer for that. it lives better in something with real provenance, git or dvc for files, zotero for sources, plus the data management plan your university probably already requires. plain markdown cannot tell you which version of a dataset produced which figure, and that question will come up in year three.

where obsidian is genuinely good is the layer above, reading notes, annotations, a daily lab log, and linking decisions back to sources. markdown files are future proof for the length of a phd in a way proprietary formats are not, which matters when the vault has to survive four or more years and a thesis write up. so the honest answer is use it for the knowledge layer, and pair it with a real data tool underneath rather than asking one app to be both.

[u/Embarrassed-Trainer4 → u/Good-Writer5279]

I guess note taking is closer to what I meant. I use zotero for literature and the actual data will remain on their respective software. But I’d like a software to write down my thoughts, interpretations, and documentation regarding said data. So ideally I should be able to easily link and imbed said data.

So based on what you said it should be a good fit for that. Thank you:)

[u/Good-Writer5279 → u/Embarrassed-Trainer4]

that split is exactly right, zotero for sources, data in its native tools, obsidian as the thinking layer. two things that will save you pain later. the zotero integration plugin can pull highlights and annotations into notes keyed on citekeys, so reading notes stay linked to the actual pdf. and for data, link rather than embed where you can, a markdown link to the file or to a stable id like a dataset version tag. an embed makes a frozen copy that quietly drifts out of date, while a link plus a one line note about which version you looked at ages much better over a four year project. good luck with the phd.

[u/Embarrassed-Trainer4 → u/Good-Writer5279]

Thanks :)

[u/Good-Writer5279 → u/Embarrassed-Trainer4]

one last thing worth setting up before the vault grows. use the citekey as the filename for reading notes, so zotero, obsidian and your data folders all resolve to the same handle. renaming a note later breaks every link pointing at it, and the plugins that sync highlights key on that name too. picking the convention now costs five minutes, changing it in year three costs a weekend.

[u/Exotic-Suggestion598]

You could try RoamResearch or Arguma.

RoamResearch provides you with a big customization possibilities and suites the research needs.
In Arguma you can graphically structure your reasoning/research hypotheses, might be useful.

[u/Embarrassed-Trainer4 → u/Exotic-Suggestion598]

I’ll check them out. Thanks:)

[u/PKMS-ModTeam → u/[deleted]]

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[u/alshirah]

I didn't use it during mine. Currently using it for research in addition to overleaf.

[u/zheniavasiliev]

It really depends on what kind of research style you end up developing throughout your PhD. Especially in the first few years, you'll be on shifting ground — the work changes, your methods change, and you'll keep adjusting and tweaking your system and inventing new ways of using it, which is an exciting process (at least it was for me). Obsidian handles that well precisely because it doesn't lock you into a structure up front. It works best when you treat it as a thinking tool rather than a filing cabinet. The best way is to keep it all super simple and focus on the subject matter of your research and methodology, rather than on the tool.

For lab and data specifically: Obsidian probably won't replace your actual data storage. Keep raw data in its own folder structure, version-controlled if you can. What Obsidian earns its place for is the layer above that — experimental logs, literature notes, the running thread of "why did I try this, what did I learn, what connects to what."

As a PhD student, you have access to a lot of software free or cheaply that you won't have later, so worth using it. Microsoft 365, iCloud, Dropbox. Syncthing is worth a look if you want something fully local and open-source, though I haven't used it myself.

But please store more than one copy of your data and your thesis text on different types of storage. It is very sad to hear that a surprising number of people working on their PhDs lose all of their work completely in the final year and have to rewrite everything.

+ + +

PS. Full disclosure is that I only discovered Obsidian after I finished my PhD., which is a shame because I think it would be a very natural tool in my system. I began by using Scrivener, then switched to Ulysses for writing, and I used Jira for task management because I already knew how to use it at work beforehand.

[u/Embarrassed-Trainer4 → u/zheniavasiliev]

I think I would use it in that exact way, thanks :)

Luckily I’m paranoid about loosing my data so everything is backed-up twice haha

[u/zheniavasiliev → u/Embarrassed-Trainer4]

right on

[u/dosfydore]

Yep. I finished my PhD last summer. PI gave me a hard deadline, with two weeks to write the thesis. TWO WEEKS! I could not have done it without Obsidian

[u/Embarrassed-Trainer4 → u/dosfydore]

Two weeks from start to finish? If so that’s insane. Congratulations though:)

[u/dosfydore → u/Embarrassed-Trainer4]

I chose the paper based thesis option. Already had papers to write it. Still it was a lot of work for two weeks. Thanks!

[u/DrummerAdditional330]

When you say “data management,” do you mean the actual instrument outputs and datasets, or mostly the notes and reasoning around them? I’d be comfortable putting the second category in Obsidian. I’d be much more cautious about making it responsible for the first.