new literature citation work flow

When I first started my first PhD the university provided EndNote free to all students, and I was delighted not to need to worry about doing the formatting for citations myself. At the time I thought it enough to just download the citation details for each paper as I got them, adding a "label" that matched the name of the folder I had downloaded it to, so I could find them later. Over time I realized that it would make sense to add a note telling my future self when and why I had downloaded each paper.

When I started my second PhD and also started using Scrivener I exported all of the citations I had in endnote and made scrivener cards for each, so that I could link to the card if I cited them in something I was writing. I also started taking reading notes directly on the cards (I was really bad about taking notes before, since if I did they would wind up being hard to find later, so I wouldn't look at them anyway, so I didn't see the point).

The longer I use Scrivener the more and more organized I am becoming. Therefore I thought I would record my current work flow for adding a new card for a paper:

1) find out about a paper. (the three most common reasons are A) seeing a scopus alert mentioning it from a previous search I had set up, B) Doing a new database search on a specific topic, C) seeing it cited in a paper I am reading.

2a) If the source is scopus (or any other on line source with the option to export the citation information export it and import the data into EndNote. Add a "label" for the primary topic, add "research notes" stating today's date and why this paper is interesting enough to make note of (this will include mentioning how I found out about it). Copy-paste the "preview" of the citation, including the research notes onto a new Scrivener card.

2b) If the source is a paper I am reading copy-paste (or re-type if the paper is so old the pdf doesn't have copyable text) the relavant quote into my reading notes for today, then make a new scrivener card, copy the citation information from the reference list of the articles and, in the notes about why I am adding the card, copy the citation quote, and add a link to the paper containing the quote. Then, add a link on the first card to the new citation. At this point either leave the new citation's card with a note that says "card added, but not downloaded", and give it a status "add to endnote" and resume reading the first article, or go looking for the article on line, download it, add it to endnote.

3) once the new paper has a card give it a list of topics, linking each one to a topic card of the same name. On each topic card include a link back to the card for the new article. Add a parenthetical note next to the link. For example my topic card "3D images" has the following list:

* Badiu, et al 2015 (pottery profiles)
* Williams et al 2019 (poster Roman cattle skulls/target practice) (see also our Email exchange on the topic)
* Williams et al 2019b (paper Roman cattle skulls) (see also our Email exchange on the topic)
* Frangione et al 2019 (automated scaling techniques-photogrammetric micro measurements)

Were each author/date is a link to that card, and the "see also our email exchange" is a link to that card. A single paper may have quite a few topics.

This is all a fair bit of extra work, but my future self will thank me for it. Indeed, I am already thanking my past self for having done this--if I am writing a grant proposal and need a citation for why a specific technique is perfect for the proposed project I need only look at the topic card for that technique, click on the links to see which of the papers that address that topic is the best one to make my case.

However, since at first I wasn't using topic cards, I am finding that as I work on my literature review and start papers I am having to go back and add topics to papers I have had for a longer time. I also have a topic card for "papers I have cited", which has come in handy when writing new papers, as I can quickly go look "what did I say last time I cited this paper?"

I suspect that my work flow will continue to evolve as I get even better at keeping good records. However, even at the first stages of using Scrivener it was already so much better than anything I had tried before. Sometimes I wonder how I managed to do research without these tools.

it needed cleaning under there anyway

Today has been a busy day. I worked from home yesterday as I didn't want the bother of going anywhere on the day I had a video job interview, but I knew that I should go to the office today, to let my colleagues know how the interview went. As luck would have it I arrived at the same time as Christina, so I was able to fill her in on the interview straight away. She confessed that she has been so busy with teaching and meetings that she had forgotten to send in the recommendation she said she'd write. I assured her that it was probably fine to get to it later this week, since they said they had a few more interviews to do before making up their minds, and that could take a couple of weeks.

Then I settled in to work, and after posting about the literature stuff I did this morning, I suddenly felt inspired to start looking again at the results from the SEM work I had done in Durham last autumn. I should have dealt with it straight away after returning (and had started to so so), but then I got the call to go to Seattle for mom's last days, and then after my return I found out about uncertainties in my job, surgery, job applications, etc. all of which made picking that part of the project back up seem kinda bothersome.

But today it was fun to work on that stuff, and I have made good progress, and am well set up to continue tomorrow. I wound up working today till 16:00, when it was time to drive David to the shop to pick up his car, which is finally repairs (for way too much money, but the list of things they replaced is huge). Afterwards we both drove to the house, he packed up the spare mattress to take to the apartment for houseguests there this week, and he drove me back to uni to get by trike and pedal home.

I had hoped to harvest the garden vegetables straight away when I got home. It dropped to +1 C last night, and my phone thought it would drop all the way to 0 C tonight and tomorrow. I wasn't certain if it would actually get cold enough long enough to do any damage to them, but I didn't see any point in risking it.

However, when I got home I was tired enough to need to curl up on the couch with a book and some popcorn first. When I had recovered enough to head out it was already 19:00, had gotten pretty dark out, and even started raining. So I put on my coveralls, grabbed the really big bucket (big enough to soak the trays from the food dehydrator) and went out.

I pulled the purple carrots first, and put them in the bottom of the bucket. Then the beets, and finally the kale. The carrots and beets completely filled the bucket, and the kale I just bundled together and brought in, roots and all. I then spent the better part of three hours cleaning it all. I wound up with two large bags full of kale leaves, one large bag of beet greens, one large bag carrot tops, one very large bag of beet root, and one bag of purple carrot. I will do something that freezes well with the greens tomorrow, as they won't last, and probably turn the beets into beetloaf this weekend.

As I worked I listened to a Swedish audio book I have listened to before whilst reading the text version at the same time. While much better in Swedish than I have been, I still prefer to have seen the text at least once before trying to listen to an audio book without reading at the same time. Since I was often running water to get dirt off of veg, I put my hearing aids onto mute.

After getting the veg into the fridge and the scrap out to the compost bin I did my yoga, and the audio book finished just as I was finishing up yoga, so I turned my hearing aids back on and started getting ready for bed. After brushing my teeth when I went out to turn of the lights I noticed that there was a faint sound coming from somewhere. It reminded my vaguely of the alarm the UPS on the server has if we have had a power outage, only much quieter. So I went downstairs, but the sound vanished as soon as I went through the curtain and started back down.

Having grown up with a hearing problem I don't have a lot of points in "which direction does the sound come from?", but after wandering around and listening various places I finally determined that was loudest in the kitchen. It was kind of hissing, and kinda squealing, kinda high pitched, and just barely loud enough to be heard, even with the hearing aids. I wondered if there was some problem with one of the electrical appliances, and went around unplugging everything I could find, but the sound didn't stop. Then I called David to ask if he had any suggestions, and, of course, he first suggested everything I had tried. Then, about the same time, we both remembered that when we got the house insurance one of the things they gave us was a small moisture sensor to put under the kitchen sink and report if there was ever a leak.

So I opened up the cupboard under the sink, pulled everything out, and found a small alarm that was, in fact making noise. I figured out how to turn it off, and set it aside whilst i cleaned up under the sink. It was, in fact, wet in there. While I had tried to be careful when washing the greens and roots it seems that while using the lift out spray nozzle that I managed to get some water down the hole where the nozzle comes out. oops! I have no idea how long the alarm had been going off. It was just barely audible (but very annoying) after I turned the sound on in my hearing aids, but while they were set to mute the outside world and pipe in the audio book there was no hope of my hearing it.

Now everything under the sink is clean and dry, and I have recorded today's adventures for posterity. Now I think I will head to bed as I had planned. Tomorrow I will return to the office to work (no choice about that really--I left my work computer there when I came home this evening, as I knew I would be too busy to do any further work today), and I hope I continue to make such good progress.