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Webinar Materials
On June 11, 2024, Amanda Sawyer from the NCBI PubMed team hosted NLM Office Hours: PubMed. The session included a presentation expanding on updates presented at the MLA Annual Conference in May 2024, showcasing what new features and improvements the PubMed team has been working on, and what’s next for PubMed. Following the presentation, Amanda was joined by Alex Sticco from the Controlled Vocabulary Services to answer questions from the audience.
Links
Transcript
>>Mike: Hi, all. Welcome to NLM office hours. It's just the top of the hour right now. We're going to give people one more minute or so to get settled in and then we'll get started. All right. Welcome everyone to our NLM office hours for June 2024. My name is Mike Davidson, I'm from the training and workforce development team here at the National Library of Medicine. My pronouns are he/him/his.
The goal is to learn more about NLM products. Today's presentation is on PubMed with national Amanda sawyer. Amanda's team development and maintain PubMed. She will be sharing some updates to PubMed as well as what you might expect to see from PubMed in the near future. We will use the rest of the session to have our panelists answer your questions.
A few quick logistical notes before we get into it. We are sharing today's session for people unable to attend or to refresh your own memory later on. The recording will be posted following the office hours. Everyone who registered will receive a link to that recording. We have a pretty decent sized crowd here, so we have muted all attendees. However, we do want to encourage you to submit your questions whenever you think of them throughout the session using the zoom Q&A feature. You should be able to find that near the bottom of your zoom window.
When we get into the question-and-answer portion I will use those to direct them to the right panelists and they will answer verbally. We may be using the chat feature to share links to helpful resources but ask you to post your questions using that Q&A tool so we can make sure to get to as many of them as possible. Before we start addressing your questions, I'm going to hand things over to Amanda Sawyer to bring us up to speed with what's new on PubMed. Amanda.
>> Amanda: Thanks, Mike. I'm Amanda Sawyer. My pronouns are she/her/hers. I'm a contractor for the PubMed team. Thank you for joining us for PubMed's office hours. As many of you know, every year we provide an update on PubMed improvements from the previous year at the medical library association's annual conference. We want that update to be available to everyone regardless of whether you are able to make it to MLA or not. That's why we're having today's webinar.
Today I will be sharing a presentation that is based off of that same presentation I gave at MLA last month. But it also includes some new information that we haven't shared yet. So, I'll share info about some new updates and features in PubMed, we'll close out with some information about where you can find training and support and like Mike said, we'll be leaving most of the time at the end of this presentation to answer any questions that you might have about PubMed. So, we'll dive into today's overview of PubMed by looking at some of PubMed's growth over the past year.
PubMed now includes more than 37 million citations, 28 million of those which link directly to the full text. 1.5 million citations were added to PubMed in the last year. Well over 1.5. More than 1.6 million have been added since MLA 2023. Our user base is growing too. The site is averaging over 3.5 million users on a typical weekday. Those users are coming from all over the world, from every continent.
They are conducting 5.5 million searches per day in the web interface alone again on an average weekday. That's not including any searches being done in the API. It's not including any of the people who are accessing PubMed data through the FDP. That's just the website. So now let's take a look at some of the new features and improvements from PubMed that were implemented over the last year.
First, we'll talk about an update to the display options for your search results. We updated the display options menu to it easier and faster to change the sort order of the results. The sort drop down menu that you can use has been moved out of display options and now appears as a stand-alone feature at the top of the search results page that you see highlighted here in a red box.
Next, I'll talk about an improvement we made to proximity searching. When we first introduced proximity searching to PubMed in November 2022 it was only available in the title and title abstract fields. Last Summer 2023 after we received some feedback from the user community, we released an update to expand proximity searching to the affiliation field as well. So, with this update you can now use a proximity search to look for multiple terms appearing in the same affiliation without requiring an exact phrase match. Since the same institution can often be represented in many different ways in affiliation data using a proximity search can be useful for this use case.
Another useful case for this feature is wherever you're doing a search and use a value of 1,000 or less, it will search for your double quoted terms together within the same affiliation rather than spread across any affiliations on the record. So, if you've done affiliation searches in the past and you're combining together terms that you know appear in the same affiliation, you know, like Bloomberg school of public health and then Baltimore without a proximity you might get those terms found spread out across multiple affiliations. If you use proximity for this, it will only look in the same affiliation line. That can be another useful case for proximity searching for you.
This was an exciting update that we just made a few weeks ago. It was announced at MLA. You can now find the technical bulletin announcement about this as well online. But we recently released an exciting update to the search syntax expanding the functionality of the asterisk wildcard character. Previously it was only used to search for alternate endings.
With this update it can be used in the middle of a term or phrase. For example, when searching for the word color if you place an asterisk in the middle of it, the search will return the British and American spellings of the word color. Additionally, multiple wildcards can now be used in the term or phrase. For example, you can use an asterisk in the phase at the end of each year such as vaccine schedule to capture vaccination schedule, vaccine scheduling, et cetera. Wildcards provide another useful tool in your search toolbox. We encourage you to use caution when you're implementing this type of search strategy.
So just for an example, that first example I showed you with the world color, it can be helpful for capturing spelling variations but placing a wildcard in the middle of the world color will also return words like colonizer, colorimeter, and Colomer. Depending on your search case it might be more helpful to rely on automatic term mapping to account for spelling variations instead of using a wildcard in this case. So, play around with it. See what cases it works well for you. As you experiment with this expanded syntax, we would love to hear your use cases and your feedback on this new feature. Please write to the help desk to share any cases where you find this feature particularly helpful. As always, if you have questions about this or any other feature in PubMed, write to the help desk and we'll be happy to investigate for you.
I'm also going to take a moment today to touch on some updates that were recently made to mesh indexing of MEDLINE citations in PubMed. I'm going to take a step back and provide background about automatic indexing. The transition to full automation was completed two years ago in April of 2022. And we did this because for many years prior to automating the volume of published literature had out stripped our ability to index it in a timely fashion. At the height of that backlog of unindexed records there were nearly 850,000 articles that were waiting to be indexed. That backlog was effectively eliminated by automating indexes. The lag time when an article first appeared in PubMed and when it received indexing had been one to three months. Now it's just a single day.
So, this diagram here on my slide shows you the current process for MEDLINE indexing. First new citations are uploaded to PubMed every day. Within 24 hours of intake to the PubMed database MEDLINE citations are indexed by our indexing algorithm. And then a subset of those indexed citations undergoes human curation for quality assurance, typically within two weeks of being added to PubMed. Since 2022 citations were being indexed with a rule-based algorithm called MTIA.
Then in April 2024, April of this year, citations began to be indexed by our new algorithm that is called MTIX. MTIX is a machine learning model known as a neural network. This updated algorithm outperforms the other algorithm being used for indexing. For details about how this algorithm works, and you can see some of the data here on my slide, as well as for other information about MEDLINE indexing, I want to point you towards the NLM office hours recording that was from February of this year. That session included NLM indexing staff providing a detailed presentation on MEDLINE indexing as well as this updated algorithm. It's a fantastic resource for learning more about how indexing works as well as specifics about the algorithm. And then if that doesn't answer all of your questions, as always, I will direct you to the NLM help desk so that indexing staff can answer your questions.
This next update that I'll touch on applies to both the PubMed and PubMed Central databases. NLM resources like PubMed and PMC have fairly large and diverse user bases including students and journalists and the general public. As well as researchers, clinician’s nations and libraries. Recognizing these have different familiarities with NLM's position as a library that collects content published by other organizations, we've been experimenting with ways to provide more context about this relationship.
In the past year, the National Library of Medicine worked to clarify the role of NLM as a library in the digital world. So, these updates include the addition of a link on all PubMed citations to a statement that clarifying that NLM is not a publisher but rather a library that collects, indexes and archives scientific literature that's been published by other organizations. We've also added a prominent note describing this relationship on all PubMed central articles as well. And additionally, we updated the default social media image when content is shared from one of NLM's literature databases to include that context as well.
I'm very excited to share this next update which will be coming very soon to your search results view in PubMed. You are hearing this announcement for the first time here today. No one has heard about this correct. For comment correction types including article updates, retraction and republications will receive a link to their related citations in your search results summary display. For example, a pre-print citation that's linked to a published journal article will include a link to the related articles PubMed citation when available.
So, you can see here in this screenshot that first citation, it is a pre-print that has subsequently been published in a journal. Once this update goes live, you'll be able to click the link here, this blue text will be a link to take you directly to that updated citation. That will show in your search results rather than going into the abstract to see that. That will contain that information. We expect this to be released in the -- coming weeks. So, keep a look out for an update when it goes live in PubMed.
As far as other things coming up next updates to PubMed website includes ongoing maintenance work.
This can mean things like software and security updates as well as bug fixes, some of which we learn about from folks like you. So, thank you for writing to the help desk when you notice something acting strangely in PubMed. We are also continuing our focus on making incremental updates to PubMed to make sure it's accessible for all our users.
We're also excited to share that we have an update coming very soon to the sidebar filter interface as well. We started looking into this update based on the feedback that we received via the help desk as well as comments that we collected at MLA in 2023. We spent several months conducting usability testing for this update with PubMed users from different backgrounds including medical librarians, clinician and a scientist among others.
One goal of this update is to make it easier to find and apply filters in the additional filters category.
We currently anticipate releasing this update over the Summer so, again, keep an eye on the technical bulletin as well as the new window or RSS feed for these announcements when the filter improvements go live in PubMed. So now I'll mention those resources about training and where you can find more information before we wrap up and move to questions.
NLM's literature resources like PubMed and PMC are always evolving. There’re a few places we encourage you to follow to stay up to date. The NLM technical bulletin provides updates and those include detailed descriptions on how the new features work. The new and noteworthy feed is a great way to stay up to date specifically about PubMed while you can file the PMC feed for PMC updates.
I also want to direct your attention to where you and your patrons can find new information. If you're looking for more information about how PubMed works or a drainer -- trainer directing others to this information tech out the PubMed user guide and FAQ linked here on the slides. You can also find it linked on every page in PubMed. We offer a variety of PubMed tutorials as well as a kit that has handouts, slides and other resources you might find useful for your work. But if you don't see an answer to your question in the user guide, or if you notice a bug or that PubMed seems to be performing strangely or if you have feedback for us on PubMed, we encourage you to reach out to the help desk.
A lot of the features that we added or updated in PubMed over the past year were based on our user feedback. We're able to use that information in our planning and developing process. You can reach the PubMed customer service team including myself as well as my colleagues on this call using that help link that you'll find at the bottom of every page in PubMed or by using this link you see here on the slide. With that, I will say thank you as always for helping us improve PubMed and hand it back to Mike to get into some of your questions.
>> Mike: Thank you so much, Amanda. We're now going to spend the rest of our time answering as many of your questions as possible. We had a few folks submit questions to us ahead of time which we greatly appreciate. I already see a bunch of fantastic questions in the Q&A panel so we're off to a good start. Please keep submitting those questions that you have in the Q&A box. I'll read them out to your panel and have them answer your questions verbally.
Speaking of our panel, a brief introduction before I start requesting -- asking them your questions. In addition to Amanda our panel includes Marie Collins of the NCBI PubMed team, Alex who is team lead for automation and strategic analysis in our controlled vocabulary services program. She would be able to help out with questions related to MEDLINE indexing. And Kate Majewski, my colleague from the Training and Workforce Development team. And also, I did not mention before Brittney Davis who is helping us out with the tech and production side of things. Between all these knowledgeable folks we should be hopefully able to answer any PubMed questions you might have.
I've seen a bunch of great PubMed questions already. I'm going to let Amanda take a breather for a second and catch her breath. This question is probably going to be handled by Alex from David. How is it decided which citations are reviewed by human indexers?
>> Alex: Yeah. So, the citations that are reviewed by human indexers are based on a set of principles that we have developed because of user impact. So, they include the things that we think are the highest priority to searchers and that's why we review them. So those are certain publication types like systemic reviews, med analysis and clinical trials. And also, the check tags are another thing that we look at on those citations. We look for new terms that we're worried may be being used incorrectly because they are new. Also, a variety of other things that we know are of high value to our users. So that's what determines those, and they get sorted into sort of a system of buckets if they meet any of the criteria, if automatic indexing has added certain terms or publishers added certain terms when they submit to PubMed those are the ones reviewed.
>> Mike: Thank you so much. All right. Amanda, we have, as you would expect, quite a few questions about wildcards. So, we're going to do a couple of rapid-fire ones of those from both Caroline and Elizabeth asked similar versions of this question. Will NLM consider extending the proximity search feature to include truncation or wildcards?
>> Amanda: So, we are aware that this is something that would be helpful and that users really want. Right now, we're not able to offer it due to technical limitations. But it's great to get this feedback so please don't stop telling us that it's useful for you just because right now we're not able to offer it. But at the moment it is a technical limitation that we're not able to provide truncation with proximity searching in PubMed.
>>Mike: On a similar note, with the expanded wildcard, Donna is asking, now that there's expanded wildcard has the number of wildcards expanded? Our team has run into messages where the limit of wildcards has been met.
>> Amanda: The answer to this is similar in that the current limitations for wildcard searching in PubMed are due to technical constraints and not something that we're able to offer right now. Again, it's really helpful for us to get your feedback and especially when you share specific use cases for what you're searching for so that we know what you'd like to see addressed and we're able to keep testing things and address them in the future if and when we are able to do so. I'll just say I saw a few comments about, like, British American spellings and that sort of thing. I'll just remind you; I realize that's just one example. There may be other cases. I'll just remind you that this is what PubMed's mapping file is for and automatic term mapping is meant to address those sorts of situations.
>> Mike: Yeah. That's a great thing to remember. And I think that the comment that you saw has that as part of the question, but I'll also is the rest of it here. Ellen is asking are there plans to have the wildcard search for a limited number of letters? So wild card that can be specified to be only one letter, one character or two characters or whatever?
>> Amanda: Yes. Unfortunately, it's exactly the same answer for that one as well. That we're aware that this is something that users want and at the moment we're not able to offer it due to technical limitations.
>> Mike: All right. That's enough of that for now. I know that there are more proximity end-to-end wildcard questions in there, so we'll come back to that in a minute. I want to change gears because a couple of people were asking you to repeat: what type of publications will have citation linking?
>> Amanda: Yes. Let me pull that list up in front of me. So, there's four types that will be linked in your search results now that includes update in, retraction in, retracted and republished in and corrected and republished in.
>> Mike: Awesome. All right. Thank you for that. And if there's other questions about that, please drop them in the Q&A. Let's see. Here's a question. Actually, Kate, I think you might be a good one to answer this. I know you worked on the pre-print-- pilot a lot. Ellen is asking how are pre-prints selected for PubMed?
>> Kate: Thanks for the question. The pilot includes four eligible pre-print servers. I'm going to put a link in chat where you can learn all about how we determined eligibility for those servers. But in terms of individual articles, we are including articles that acknowledge direct NIH support or -- and/or have an NIH affiliated author. So, here's the link to this scope of the pilot. Thanks.
>> Mike: All right. Thank you for that. I'm taking a look through here. I'm going to cycle back to the wildcard question because somebody was asking a follow-up about the limit of the number of wildcard operators allowed per search. Amanda, do you happen to know that?
>> Amanda: Let me double check on the number but I'm pretty sure it's 256.
>> Mike: Yes. Actually I'm -- I'm seeing a message from Jessica also.
>> Amanda: Perfect. I pulled that off the top of my head. It's currently 256 wildcards per query. This is in place to ensure fast and reliable system performance. If you think back to the beginning of my presentation I talked about 3.5 million searches per day. That 256 number came out of a bunch of testing of what we need to limit to ensure that PubMed continues to perform for all of those users and those millions of searchers. I'll just add in case you were asking about the limit for the root characters as well, you have to have at least four characters before an asterisk because I know that's being asked about earlier as well. So, I'll just mention both limits right now.
>> Mike: Excellent. Thank you for that. All right. Alex, I think it's time we -- we go back to you because we have indexing questions here. Mary Jane is asking now that MEDLINE is fully automated is NLM considering updates to add newer terms to older records?
>> Alex: Yes, that is something that we've considered. So, I think that we are certainly planning to use MTIX to do with MTIA. Because we know the MTIX is superior there. We are planning for that. Many were curated by humans after they were indention decks -- indexed so we don't want to overwrite the curation. So, there are some reasons we haven't moved that forward yet, but we are looking at it. As for even sort of older things so that we could get sort of newer mesh terms on to articles about those things that were published before those mesh terms were available, that's something that we are going to have to look at kind of an a case by case basis because, you know, MTX getting -- getting things wrong sometimes and we don't want to add noise into PubMed's searches.
I think what we have to do in that case is sort of look at for each kind of individual term --this gets hard to do for each individual term. So, we might limit this kind of project to sort of high impact terms like publication types or something. But we are looking at where's the sort of cut-off where we can trust the MTIX actually really knows this term is correct. So, it gives a score to each term when it indexes it. For example, for systemic reviews if it scores above an 8 it's right, you know, like 99.99% of the time. So we can say, you know, if we go back and index with systemic review that if it's -- you know, as long as we cut off the score at an appropriate point that we could trust that this indexing would be accurate and we could add it to a bunch of other, you know, things, articles where it's been either missed or where it wasn't available at the time that the article was indexed. So, it is something we're looking at. It would be a very big project to do that in a way where we could trust that it's reliable. It may be something that we do down the line. It's a good idea. It is not something that is going to happen any time really soon.
>> Mike: Yeah, that's a good point. That sort of underscores a lot of how we think about this stuff. Which is -- there's a lot of things that we would like to do and that seem on the face they are a good idea. And even are a good idea. We want to make sure that we are doing them with the due considers so we're not, you know, solving a small problem but causing a big one or causing other people, you know -- creating different problems as we go about this.
So, Alex and the folks over who work on indexing are very cognizant of this, like, be measured, be cautious, make sure that we're making the right decisions. All right. I'll see what other questions we have here. We've been pretty efficient about going through these questions. So, if you have more questions, please feel free to throw them in the Q and A. I think we should definitely have time for more than we have in there. So, I'm going to go to Amanda on this one. Margaret was asking, are you planning to add comment on as one of the publication types now noted in the search results? I guess for the new related feature.
>> Amanda: Sure, that's a great question. So, the four that we're starting out with, these are the four that have previously already been noted in search results as labels. Even though we haven't put this update into production yet in PubMed you can see these four labels in your search results already, they are just not clickable. So, we are expanding this feature to add those hyperlinks to them to make it easier to access related articles. Those four types of related article links were selected because they provide really important context when you're viewing your search results. Like you want to know if something has been retracted or if you see a pre-print citation it's really important that you know immediately if that's been updated or not. And we're trying to keep search results primarily showing just that most important info so that it stays easy to scan and we're not overloading your search results with extra information. So, we started with those four. But we'll be watching for feedback about this feature. If you have use cases for additional ones that you think would be helpful for you, please do let us know. We'll be looking out for that information.
>> Mike: Yeah. Thank you. That sort of goes along with what we were talking about measured impact. Anything that effects that search results page, which is why a lot of these features that, you know, Amanda said we're working on this, we want to make sure this is right and we're doing it either in small steps or at least being very considerate about the changes we're making with lots of testing. So, all right.
I'm going to go back to Alex now. Sarah was asking, where's the best place to find information on the new system used for mesh indexes in PubMed? How it's different than the previous method. I know we talked about this a little bit in the previous office hours but Alex, I think you had some resources for that.
>> Alex: Right. So, the previous office hours are a good resource for that. We do discuss if you want sort after an explicit comparison between the previous method and the new method that office hours presentation is definitely going to be the best resource. I'm sure that we can put the link to that in the chat some place. The other places that you can find out more about MTIX are the indexer FAQ pages online. And we can put that link into chat. It's at NLM.nih.gov. There's also a paper on MTIX if you want really technical details about how -- you know, what that algorithm, the different layers of the model and what that consists of. And the sort of original experiments. The model has been refined to a certain extent beyond that but the basics of how it works are all still as outlined in that paper. So it would be, you know, sort of minor differences in training and special components that or rules that we use for filtering and things like that. Not wide divergence from what is described in the paper. So, we can link to the paper as well.
>> Mike: Excellent. Yeah, we'll get those linked in the chat in the next few moments. While I have you Alex, Sue is asking a question -- this is sort of related to our discussion before about retrospective indexing and going back and using MTIX to do things that couldn't be done earlier. Could MTIX index citations from digitalized pre-1946 to add content to old MEDLINE?
>> Alex: We did do that with MTIA at one point with the sort of theory being it's better to have something on those articles than nothing for retrieval. And we could look at doing that with MTIX. One unknown there is how much MXIX's performance will degrade when it's looking at older language. So, you know, it's trained on a set -- on the set of articles from MEDLINE from 2007 to 2022. And the language in 1945 could be really substantially different and we don't know what its performance would look like under those circumstances. So that would be something that I think we would need to investigate more. It's obviously a possibility. I don't think we've had a lot of people express demand for that so it's not something we've prioritized. We would definitely be interested to hear from people if there's demand for that if it's something we should be pursuing.
>> Mike: And I'm just trying to think back. I've looked at some of that old MEDLINE stuff as well. And I think a lot of that doesn't have abstracts. So, I feel like MTIX would have just as much difficulty as a human would assessing what mesh settings to add to it based just on the title in the journal. So that might be another factor that could cause a problem there.
>> Alex: Yeah. One thing that we're finding is that the amount of input it gets is pretty significant. It's really expecting to see a title and an abstract and date and journal name. If it doesn't have any of those things it behaves in sort of unpredictable ways. So, we are -- it would really depend on the information that is available there. It actually performs pretty well from meaningful titles. As long as the title has something that has, like, actual medical language in it, the indexes are surprisingly good from just the title. But if the title is something very brief it starts getting wonky.
>> Mike: Awesome. Thank you for that. All right. Let me go back to Amanda on this one. Helena is commenting about the nursing journal filter. Please bring back the nursing journal filter. It is still the most requested Filter here at my hospital. Amanda, you want to address that a little bit?
>> Amanda: It was built on a specialized query that was pretty labor-intensive to build and then to keep up to date. Keeping it up to date is really the key point here. It's no longer sustainable for us to continue updating that. So, when NLM announced that those subsets would no longer be updated anymore we removed them from the PubMed interface. Leaving out of date filters on PubMed is dangerous in our opinion. It potentially exposed relevant citations to your searchers and misleading to users who didn't know those queries were updated recently. What I can say to hopefully help you in your job is the latest versions of those queries are available to use and modify yourself and you can build your own custom filters using the NCBI account. I know there are libraries that have done -- libraries that have done that and created resources as well. If you would like help crafting a specific query definitely encourage you to write to the help desk because our reference team can help you with that.
>> Mike: All right. Thank you so much for that. Speaking of writing to the help desk, I have a question that may be better addressed there but I'll mention it because Leighton was asking it. We notice that the FTP of new records jumped from a couple of hundred last week to 20,000 last week. Have any of the changes you described today impacted the FTP feed?
>> Amanda: So, my instinct is to say no, none of the changes I described today should have impacted that. I would like you to write to the help desk. This sounds like a really specific question I may need to get some help from other of my team members to get help answering. Do send us a message at the help desk and we will investigate that as soon as possible.
>> Mike: Caroline has a question; our back room has crowd sourced when you've been answering questions. Caroline is asking about the ratio or percentage of indexed articles to non-indexed articles in PubMed. Based on our quick back of the napkin path 84% of PubMed articles are indexed with mesh. It's about 31 million out of about 37 million. So that's the numbers that we have here. All right.
And, oh, Carol is asking, this is a question maybe Kate can address because it has to do with our many training products. Oh, Sarah is asking about this as well. Could you share a link to the recording of the previous office hours?
>> Kate: Thanks so much, both of you, for giving me the opportunity to link to our NLM learning resources database. I put the link in the chat. On the right-hand side there's a link to NLM office hours recordings. You will see a menu on the right that highlights some of our training resources. So, take a look at the other stuff too. There's a link to the office hours recordings there.
>> Mike: All right. Thank you for that. I'm going to just take a quick look through here. We definitely still have some more time. If there's questions that people want to ask, we should be able to get to a few more here. Let's see what we can see. Debra is asking, is there a way to learn what nursing journals have been added to the list of MEDLINE index journals since the nursing filter stopped being updated? Amanda, I saw you put a link to topic-specific queries in the chat. If you have further information on that.
>> Amanda: That is a great question. That I don't think I have an answer to right now. I don't know if anyone else on the call has an answer. But if not, I would say write to the help desk. This is something that our reference staff might be help to able you with and if not, it will be sent to us at PubMed, and we can talk about it.
>> Mike: One approach that I know can be used, it takes a little bit of work, is searching in the NLM catalog database. For MEDLINE journals. I don't have a screen up that I can share right now. But let me see if I can get that figured out. While we're looking through any other questions. Again, if anybody has any other questions, please feel free to drop them in. Maybe we can get an answer to that. A more fulsome answer to that later on today. All right. Molly is asking, are there any new things on the horizon for PubMed and NLM that you can share? So, I know we've talked a little bit about some of that stuff. Maybe if you wanted to talk more about the filters process and how that's going.
>> Amanda: Sure. Yeah. Always happy to talk about filters update that's coming. That is the next major change that we have coming for PubMed as I mentioned. So, we're finished with our usability testing stage and are in the process of implementing those into the interface. And part of that taking a while is that we do some pretty thorough testing to ensure the changes we make don't impact other areas of the website. So, I don't have an exact timeline to share on that but what I can share is that some of the biggest changes that we think you'll notice to the new filters interface are streamlining how you -- apply those additional filters in the menu an additional filters menu pops up. It will make it easier to find them and apply them to your search as well.
We're also doing some refinement to the custom date range filter. There are some validation rules that you have to follow when you enter dates into this. We're trying to make this a little bit easier to use. So, for example, once this update is in place you'll be able to enter the same year to search for a specific one-year period. So, the same year in both fields to search a specific one-year period after we make this update. And I also just want to emphasize that we're keeping the focus on this improvement on the most heavily used filters and making sure that these remain very easy for you to use. I'll also clarify just so everyone knows that this is an update to the interface itself and how you can apply filters from that interface. But there's no change to the filters themselves and how they function in your PubMed search. So, it should not change your search results and won't change the way you expect those filters to work.
>> Mike: All right. Thank you so much for that. I'm really excited to see it too. I know that -- improvements to filters have been something that people have been asking for a long time. So, I'm excited to see sort of what we come up with. Obviously as we everything, PubMed is never done, right. So, whatever the first version of this you see is, you know, we're still always going to be looking to iterate and improve and develop further what we can offer. All right. While you were giving that answer I think I found a way to share my screen. So, bear with me one moment and I will open that up. I was not prepared to share. I was just going to be moderating. All right. I think that you should be able to see this.
So, there's a number of different ways to get to the NLM catalog database. Just from PubMed one way to go about it is click on the mesh database link down here. Then just change your drop down here from mesh to NLM catalog. And this is not a full proof way, but this is a good way of figuring out what sort of things are being, what sort of journals are being indexed from MEDLINE. So, I'll just type in nursing right now as an example. This is not necessarily the best version of this search. This gives you everything in this NLM catalog database on nursing. That will give you -- will restrict your search from nursing just to this. Now, again, doing a search for nursing is not necessarily going to get you everything, every journal that has nursing content.
So, you have to experiment a little bit on your own. Using the NLM catalog is a good way of figuring out at least what journals are being indexed because of this side filter here. All right. Let me get back to my moderator job and look more at these questions. All right. Still have a few more minutes to go. Again, if anybody else has any other questions that we have not addressed, we'd be happy to do that. From Mia, is there any way that the filter can be changed so when you go to select show the filter gets checked automatically? This is back to your discussion of the new filters redesign.
>> Amanda: Absolutely. This was a pain point that we heard from a lot of users and the feedback that prompted us to go and look -- looking at the filter interface again. We are aware that the process is selecting and applying a filter took many steps. The update that we are going to release here soon is intended to address that pain point. So, I can't give you specifics on how it's going to work because like I said we are still testing it and I don't want to promise something in case, you know, the testing comes out -- we have to work around something. But that is what we are working on and why this review came up in the first place.
>> Mike: Yeah. Excellent. I know that that's something that people have been talking about for some time. All right. Let's see. Actually, we have a couple more questions here. Again, we still have time for a few more to feel free to drop any extra ones in there. I'm just pulling up one. Information on one answer here. So, while we're doing that, Kate, do you want to maybe give us some highlights of other upcoming opportunities?
>> Kate: I would definitely like to share that in July we have how PubMed works coming up. So please join us. I'm going to put a link in chat to our help PubMed works series. It's a four-part online interactive class. We actually offer an on-demand session as well if you can't make our July session, but we hope you can join us. We also have a variety of just in time training resources that you can find through that learning resources database that I just linked to or there's a specific guide just for PubMed training. I'll put that link in chat as well.
>> Mike: Excellent. I usually do what’s coming up in PubMed training right at the end and then we put all the links in chat and then the session ends so nobody gets a chance to actually click on them. So, I wanted to make sure we got to that first. Let's see. Two more questions here that are in here. I think we can definitely get to both of those and maybe one or two more quick questions so if anybody else has any last ones we'll get those addressed as well. I'll just deal with the filters one first really quick. Molly is asking, will users need to update their current myNCBI saved searches?
>> Amanda: So, there aren't any changes to how the filters themselves work and we're not renaming any filters. So, I wouldn't expect you to have any issues with your myNCBI saved searches after this update. If you do or if you get some error message, please do write to us. You may -- something that users might encounter is if you haven't cleared your cache, you might get a message this has been moved or doesn't exist anymore. The solution is to clear your browser history once the update is out and try again. That's not tied to your saved searches, that's just your browser remembering how it works. If you encounter any issues with your saved searches or anything else, please write to us and we'll be happy to investigate and help you fix any issues you encounter.
>> Mike: And, now that you've specifically mentioned that, I feel like that's something we'll make sure that we test, do some testing on before we launch anything.
>> Amanda: Absolutely. Yeah, yeah, that's definitely in our list of testing. Definitely in our list of testing.
>> Mike: Carol is asking, are there articles that are indexed with mesh that are not from MEDLINE journals? Which is kind of a tricky question. Alex, I think, do you want to handle this one?
>> Alex: Yeah. So, we only index MEDLINE journals. So, there won't be any articles indexed that aren't from MEDLINE journals, but there may be articles indexed from journals no longer MEDLINE journals. Journals that have been discontinued, journals that have been taken over or continued by a different publication or journals deselected from MEDLINE may have articles that were indexed previously while they were MEDLINE journals. That's the only time you will find indexed articles from journals that are not current MEDLINE journals is when they previously were.
>> Mike: Excellent. Thank you for that. It looks like Sandy has a question here that this might be something that we can't address fully in this office hours. But I'll bring it up. Amanda, if, if this is a if this is a right to another right to the help desk, then I think that might be the best way to handle this.Sandy is saying they have extreme difficulty getting logged into myNCBI. They've updated to the third-party login. Sometimes, you have to try at least five times before getting logged in to the help desk. That's the way to go for that one?
>> Amanda: That does sound incredibly frustrating. Please do write to the help desk. There's another team that handles the My NCBI login and they are the best people to answer that question for you and they should be able to walk through the process with you and hopefully identify whatever the issue is.
>> Mike: And I say this because I like to say this at every office hour, the number of times we say write to the help desk about something does seem very high and can sometimes seem like we are putting things off. The people who are going to answer those help desk questions are all of these panelists who are on this call right now. We are the ones who look at these things. Getting that information and being able to help you rather than just having you unhappy about something makes our job easier, right? It makes it much easier to address the problems, make sure other people aren't having those problems. That comments and questions that get written in we read them, we respond to them, we do our best to help you that way. So, I know that sometimes sort of writing to customer service seems like a black box that goes nowhere. But for us, like again this is the way that we -- the best way for us to hear from you and the best way for us to get you the help that you need.
>> Amanda: I’ll also add to that that when you provide feedback through the help desk to us then we have a record of your feedback in writing and we're able to see how many people ask about specific features, we have records of your use cases. So, if technical limitations change in the future we can go back and say, I know this person had this use case, can we address this now. So having that written record of the feedback you're giving to us is very, very useful for us as well do development. So, I know that it feels -- I can understand that it feels a little frustrating to keep writing many about -- writing in about truncation or proximity but it really is very useful for us when we are making improvements or doing research on what areas we can make improvements in if we have those written records from you. It's very helpful.
>> Mike: Yeah. Especially in a time when we're seeing people face-to-face a lot less too. You know, we don't have as many avenues and conferences where we are hearing from people. Donna, very nice, Donna. Donna said our experience with the help desk has always been a good experience. Thank you very much. Very nice to hear. All right. I think that we're just about out of time. Unfortunately, Janet, sorry, there's not enough time for me to tell you the back story on my wife's horse collection that you can see in my background here. So, I think we're going to wrap up here.
Thank you all tremendously for all of the fantastic questions that you sent our way today and for taking the time to ask them and to come hear what we have to say. Thank you to our panelists and Amanda especially for that great presentation. Brittney will be posting a link in the chat which will get you to a short evaluation survey regarding today's session. That should also open up automatically once you exit the zoom. So, if you don't get it in the chat, you should be able to get it once the session closes.
If you're interested in receiving MLA CE credit, make sure that you fill out that survey because that is going to give you access to the code you need to claim the credit. Even If you're not interested in MLA CE credit, please fill out that survey. Getting that information about sort of our training, you know, what you like, what you don't like, what else we can do, what else we can offer you is really helpful and really helps guide how we are able to deliver training opportunities to you. So, with that said, I think that we're -- we have about five minutes -- out the door five minutes early.
So, thank you once again to our panelists, to our attendees, to all of our PubMed users, and we'll see you next time.
Last Reviewed: June 11, 2024