Effective Literature Research with Europe PMC

hello everyone welcome to this webinar on effective literature research my name is Maria left Rinku and I work at the European bioinformatics Institute in Kingston I'm part of the team that develops here at PMC database for research literature and today we're gonna learn about useful tips and tricks for effective literature research this webinar is aimed at scientists who feel overwhelmed by the volume of new information and those who don't really want to miss an important paper on their topic I am a trained scientist myself and I know that it can be challenging at times to keep up with the growing amount of papers in your field please note that we are expecting that you're already familiar with some basic principles of literature searches and we will not go into different ways of defining the search parameters instead in this webinar we will explore different tools that are available to you from your PMC to make your search for scientific papers more efficient and less time-consuming we will touch on a lot of your PMC features and if you want to explore some of these in more detail I will be posting links to other training materials as we go along if you have questions at any point during this webinar please post them to the chat box and we will have a Q&A session at the end so what will we cover today we will start with a brief introduction for your PMC so that it's clear what content is available to you on the your PMC website we will then look at a typical search by keyword and explore how you can tailor it to get the most relevant results using different filters we will also demonstrate how you can sort retrieved papers to prioritize your reading list next we will show you how to find a specific paper that you might have in mind using bibliographic information and by that I mean a journal or author name with the help of advanced search we will have a separate section dedicated to author searches these are quite popular and can be difficult for authors with common names we will also touch on a specific search for publications that report research data and show you how to find publications that mention clinical trials protein structures or a particular data set like we Gina I will not have time to cover managing your searches for example having a complex search like the one we will learn to configure today in order to run it frequently or for example how to set up notifications for new papers on your search if you would like to learn how to do that I can suggest for you to watch our previous webinar I have put a link on this slide and you can get the link from the chat box as well our program is quite busy so let's get started first let me introduce you to your PMC your PMC is a free database of biomedical research literature your theme C is based at the European bioinformatics Institute or amble EBI and it is supported by 29 research funders including the WH o er C Wellcome Trust and others as their designated open access repository we are a partner in the PubMed Central International archive network and share full-text content with PubMed Central at the National Library of Medicine in the USA considering that content in Europe PMC is partially shared with PubMed Central USA a natural question is how's Europeans is different from PubMed and PubMed Central in addition to the expert literature sources that we make available which I'm gonna highlight in a minute your PMC offers some innovative services and features that are layered on top of the content and one of such features is a unified search if you are familiar with these repositories you will know that PubMed allows you to search research abstracts for your keywords of interest while PMC holds a free full-text collection which means that your search in PubMed excludes full-text and reciprocally your search in PubMed Central will only go through available full-text leaving behind a large collection of publications with only an abstract available Europe PMC offers a single search for all content both abstracts and full text this saves you the trouble of searching both databases and can significantly expand your search which is especially useful for narrowly defined topics in addition to content from PubMed and PMC content in Europe PMC extends beyond those two resources the bulk of the content in your PMC is made up of abstracts we have over 33 million abstracts and those come mainly from MEDLINE the database that powers PubMed but it includes some other sources for example selected Agricola abstracts which are useful for plant researchers as part of the PMC international collaboration we also hold almost 5 million articles for which we have full text supplemented with other types of content such as books patents preprints PhD theses and so on your PMC also provides detailed grant information from 29 funding organizations which includes grant abstracts with such diversity of the available content powerful search is really crucial let's see how you can fine-tune a simple topic search for papers we will explore a number of different search strategies and tools to make it easier to follow the webinar my suggestion would be that you open a new tab in your browser and go to the European see page at Europe PMC org as I introduce a new feature you can try it out directly on the website and see how it works for you we'll send the link in the chat box now now that we're all set up let's start most commonly you would use a few keywords for a topic search let's say we want to know about connection between mutations in a p53 gene and DNA damage type the keywords p53 mutation DNA damage into your search bar you can see that it retrieves nearly 25,000 publications if you were to compare this search to PubMed you would see that it retrieves about 3000 results the main reason for this is that European see searches through the full-text in addition to the abstracts but there are other technical differences that contribute to this as well indeed if you searched on PMC us say for the same string of keywords you would see a much higher number of papers different from both PubMed and your PMC all three resources provide you with a search option but as you can see the list of results would be quite different but no matter where you search you should know how the search works and how you can fine-tune it one important thing to bear in mind is that your PMC search uses boolean logic just like any other search engine boolean search uses so-called logical operators and or not to combine the keywords as you type your keywords into the search bar behind the scenes your search is transformed with a proper syntax p53 and mutation and DNA and damage your search can be modified to search for p53 or mutation not DNA and damage or any other combination using the operators to modify your search please remember to type operators in capital letters otherwise they're treated just like another keyword try it out for yourself on this slide there are a couple of examples of different boolean searches and is a default in most cases you do not need to manually enter it with your keywords now your search can be modified and you need to remember that for that you would need brackets to group different keywords for them to be processed as unit in this particular case you will search for documents that contain words p53 and mutation but don't contain either word DNA or word damaged so brackets help you group things and treat them as a set here is an example of even more complex boolean use we are searching for papers on adaptations of a group of animals that includes whales dolphins and porpoises and is commonly known under a Latin name citta Xie I'm not sure I'm pronouncing that right but bear with me so we're not interested in adaptations for decompression we would like to exclude that and our search will look like this citation or whale or dolphin or porpoise in brackets followed by and adaptation not decompression in this case we have to list different animals to get a more thorough list of results and it can be tricky to list them all did you miss something should you mention specific species like orcas are narwhals luckily there is a simpler way in Europe you see you can add synonyms to your search by selecting one of the filters in the advanced search page you can go to the advanced search using the link next to the search button on the main search page try it out as we go on the advanced search page you need to switch on synonym query expansion in the filter section you need to scroll down to find the filter section once you switch it on it will include synonyms for your keywords in the search for example our search for DNA damage will also include articles that mention genotoxic stress and you can see a list of synonyms for p53 your preference searching with or without synonyms will be remembered as long as you stay on the website so don't forget to change it if you want to have more defined list of results for those of you who are trying it out please switch the synonyms off again and return to the main search page in addition to synonyms your search is expanded in other ways have a closer look at the search result that is presented on this slide you will notice that it picks up p53 mutation 'el rather than p53 mutation this happens automatically and switching synonyms on and off will not affect this your query for mutation will include terms mutations mutated and mutational in addition the way that search works is that it matches individual keywords in the document but it isn't sensitive to the distance between them so p53 might be found in the introduction mutation might be found in methods and DNA damage might be stated in conclusion this means that if you search for p53 mutation you will come across results like the second example here then discusses VHL gene mutation in the p53 binding domain it is a related paper but not exactly the topic we were looking for which is a mutation of the p53 gene itself to get around this and match the word or phrase exactly put it in double quotes when you search this will force the search to return only articles where p53 mutation appears as a phrase so by now we already learned some tricks we use boolean operators and or not we learned about synonyms and we learn how to get an exact match for a keyword or phrase let's move on and talk about filters if you remember our initial search for p53 mutation DNA damage returns about 25,000 of results which is probably too broad to be of any use let's explore what tools are available to limit this to more relevant articles there are two popular filter types available from the right-hand side menu as you search content types and date other filters will be available from the advanced search page but for now let's only focus on these since they will be likely the only filters you need for majority of your searches content type filter allows you to restrict your search to specific content types while they filter you guessed it limits your search to articles published in a specific year or year range let's start with content types the first two free full-text and open access can be a bit confusing because many people believe they mean the same thing free full-text means that the article is available in Europe PMC to read open access is a subset of all three full-text articles that has a specific copyright license which allows reuse with attribution if you wanted to reuse a figure from an open access paper for your own presentation or report you could do so with proper acknowledgement without asking publisher or author for permission so once again open access is a subpopulation of free full-text available in your PMC here you can see the list of results after you have applied the free full-text filter if you click on one of your search results you will be taken to the abstract page of the article which you can see here when you write the abstract page again on the right hand side a link to the full text will be displayed I highlighted here with a green box this particular example has free full text in your PMC and you can see your PMC logo next to the full text link but for some articles you will see a link to an external website where the full-text is located most often that's the Journal website you may need subscription to read the article there now sometimes the full text of an article is not present in Europe PMC but it is still available to read for free somewhere for example if the full text is in a university repository to circumvent this we use brilliant service from anti-wall to find free full-text from other sources anti-wall is a database that harvests open access content from over 50,000 publishers and repositories if the full text is not available in Europe PMC we will search unpayable registry to see if an open access copy is instead available elsewhere if we can find it we will display a green lock icon next to the full-text button to let you know that the content is free and doesn't require subscription it allows us to bring you almost 50% more free full-text articles bringing the total to over 7 million here I just wanted to mention that when you use the free full-text filter on your search it will not pick up the Articles that we find wire unpayable so it might be too narrow to use in some cases coming back to search filters there are more content type filters that I haven't mentioned yet reviews is a pretty useful one especially if you're looking for publications that would summarize current know-how on a particular topic try selecting a reviews filter in the search bar on top of your search results you will see the search change to include review publication types sometimes you may want to focus on primary research rather than read the review we're planning to add another filter to exclude reviews from search in the nearest future but meanwhile I can suggest a quick and dirty work around it is to click on the review filter and then as we are already familiar with the boolean logic change the query in the search bar from ends to not now that's a hack but hopefully you can do it in a click of a button in just a short time now other out sorry I'll come back to this so other popular types of content are patent abstracts books and other documents so that would include for example conference proceedings or government reports and preprints free prints our research manuscripts that haven't passed peer review by topic experts they may or may not be published later on in scientific journals currently the preprint subset in your PMC is quite small but we're considering expanding it in the future so you can use all of these different content type filters to narrow your search the other type is the date filter quite often you may want to focus on more recent articles so you may want to limit the publication date range to the latest year you can also set a custom date range if you wanted to include publications within specific period say last two or five years another way to look at the most recent research is actually to apply a different sort order so with this we transition from filters to sorting your search results there are several ways to serve them in Europe PMC when you carry out a search in your at PMC the sort by options are shown at the top of the results list the default is always relevant sort order almost every search engine is using the relevant sorting but do you actually know how relevance is defined in your PMC relevant sorting takes them to account the frequency with which the search term is found in the text the more time someone is talking about p53 the higher are the chances that p53 will be the focus of that particular publication so it will be more relevant to your search among other things there can be numerous different ideas that we have to include when defining relevance for example rare words receive a higher score than the common ones so an article that mentions p53 five times and mutation only ones would be scoring higher than an article that mentions mutation five times and p53 only once because p53 happens to be much rarer in the scientific articles than mutations CAD mutations can apply to many different genes at the same time finally we also factor in the publication date so in the relevant sort order more freshly published articles will be still found closer to the top of the list but if you wanted to actually sort by publication date you can use the date sort option it's especially useful for searches that you run frequently and when you don't want to see articles that you have already read you can view the most recently published records if you click on the date sort option here I must warn you you cannot combine two sort orders you cannot select most recent and most relevant articles as a workaround you can use the date filter that we tried out before in combination with relevant sorting to limit your search to a most recent year or two but within your results list individual articles will still be sorted by relevance and not by date if you click on the date sort option again you can view the records in ascending date order to get the oldest publications on the topic like this 1983 article records in Europe PMC date as far as 1781 it can be handy if you want to see how a field has developed or if you would like to find a classical article note that since we're not using relevance as a sort order anymore we might be getting results like the subject index which is probably not exactly what we were looking initially one way to quickly judge whether a result is relevant to your search is to use snippets snippets are short extracts from the article that contain your search keywords they show you where your keywords appear in the text you're possibly familiar with snippets from searches on google snippets can help you see why this particular record was picked up by your search and decide if you want to read it or skip it here is a highlight of available snippets for one of the search results you can see it in the green box I want to show you one useful feature in Europe PMC that allows you to actually follow these snippets to the precise place in the text where these are found here is how it works once you follow one of the results you will see that if the snippet is found in the abstract it is highlighted in yellow if it's found in the full text it will appear below the abstract with a go link that will bring you to the exact place in the full-text where the extract appears sometimes snippets are hard to locate because they appear in a figure table legend and in this cases you will see a notice appear finally coming back to the sword options you can serve your search results by the number by the number of times a record has been cited this can be helpful for identifying potentially most impactful articles in your search you can see the number of citations for each article in the search results since we rely on openly available content citation count in Europe PMC may be lower than the count in scopus our web of science but you don't need subscription to use your PMC besides no database is complete and even Scopus and web of science will differ from each other and from results available in Google Scholar what I can tell you is that highly cited articles in Europe PMC correlate with highly cited papers on other platforms so you can still rely on this number as a proxy notice that the number of citations is a link if you click on it it will search for articles that cite this particular publication which can be pretty useful if you're looking for ways to expand your reading list we've already covered a lot of ground exploring topic searches we learn how to use boolean synonyms exact matches popular filters like content types and date sort orders including relevance date and time cited sometimes however what you want is to find a single specific article simplest strategy is searching for an article by title or part of the title as shown this however will return many results containing the keywords we used so the simplest way to get directly to the publication is to place the title within quotation marks like we did before to find an exact match this will take you directly to the abstract page for that particular article sometimes however you may not remember the title quite often you might want to search for a publication for which we know a combination of the publication year journal name and perhaps a keyword or two the simplest strategy is to type all that into a search bar but often results can be disappointing look at this article it was published by an author called Emily blood in the journal cold blood and it contains the word blood in the text of the article so you would need to search for blood blood blood which probably won't return much useful results to have a much more precise and efficient search you can take advantage of the Advanced Search page before we get on with it I want to say that for most use cases you should be completely covered by a simple keyword search strategy and the popular filters you only might need these advanced search options if you're doing a thorough literature research for example for a review or thesis or when starting a completely different and new field you can do very precise searches for all kinds of purposes and this means that there are several different tools available in the advanced search it might get a bit overwhelming do not despair as I said this is quite advanced material but it can help you to handle tricky cases I hope that you're following through with me and if you have any questions post them to the chat box and we'll try to answer them at the end so let's come back to the advanced search as it provides a number of parameters as you might remember the link to the advanced search is right next to the search bar in the advanced search itself there will be all those different sections from bibliographic fields to external links we will not look at all of them as this is definitely too much to cover today but I will highlight some options that might be particularly useful to you and I can suggest that if you'd like to learn more about it you can browse it after the webinar and see what kind of searches you can configure remember our original task we wanted to search for a publication for which we know a combination of author perhaps publication year journal name and maybe a keyword or two let's say we want to look for an article published by Google Bailey in plus one on pumpkin transcriptome we will need to use the bibliographic field section of the advanced search we will type in the journal name the author name and one of our keywords I'll choose bumpkin in the title search field as you type in your parameters they will be reflected at the top of the advanced search page as a single query if you copy and paste the same text into the search bar you will not need to go to the advanced search page your results will be the same the advanced search form simply transforms your query into the one that the system can understand and here is the result of your search exactly the paper that we were looking for before published by Vale eagle in plus one on pumpkin transcriptome there are many other advanced search tools but the last one that I'll highlight today is section search it allows you to search for keywords in specific parts of the article full text for example in results or in method section you can find this option on the advanced search page under filters section select the section type that you're interested in and enter your keyword if you want to look for papers that discuss the application of crisper rather than primary research where crisper method is used for experiments this tool can help you fine-tune your search so far we've covered different options in the advanced search one thing that we did was to search for in publication by an author that we knew sometimes you want to search for article by fields expert collaborator or perhaps even find your own publications in this section will briefly cover author searches here is an example of a quick search for an author named John Smith your PMC automatically recognizes this as an author search and restricts results to those where the name appears in the author list the problem is that there are many authors with that name look closely at the results first one has an author with initials Smith J a and the second result is from Smith's JW all articles by Aldrin Smith's will be present in your results list presenting a problem how do you know one researcher from another this is a major problem for any author based search in this example an author search for J a Smith will return two articles with no quick and easy way to determine which article matches which author the way that your PMC's circumvents this is by using orchid IDs orchid ID is a unique ID assigned to an individual researcher if they register with the nonprofit orchid organization it allows us to distinguish authors based on a unique number their orchid ID if you look again at our results when searching for John Smith you will see a grey box at the top of the results list in the box there are two suggested authors those suggestions are based on authors who have an orchid we show up to two authors with an orchid who have the highest number of publications in Europe pmc if their affiliation is available we will also show it to you so now if you know that John east myths from university of arizona is indeed the author that you were looking for you can click on his name see how our query has immediately changed we're now searching for the author by their orchid ID and our results list includes only publications that we can be certain belong to that particular author one limitation to this approach is that it relies on two things that the author you're looking for has an orchid and that they keep their record up to date in order for us to know which articles belong to the author she or he needs to regularly claim any new articles to their profile or provide their ID to the journal during submission but there are hundreds of thousands of authors that are actively using their orchid to publish so I'm sure this fee sure can be useful to many of you if you would like to learn more about orchid how we use it in your PMC or how you could use it to highlight your own research you can watch another tutorial dedicated specifically to author services we will send a link in the chat now so we've come a long way and in the last part of this webinar we will talk about searching for linked research data that is data described or cited in the paper so what kinds of data am I talking about any article is first of all a story about data microscopy images or psychology questionnaires are two very different data types that you could find in scientific papers often the data described in the paper resides in a database protein databank hosts protein structural information the European nucleotide archive provides nucleotide sequencing information while figshare or dry it preserve outputs such as figures datasets images and videos let's say if you wanted to find an audio of a bird song that might also need a place that it can be deposited to for a reader to find this kind of data it needs to be cited in the text of the article and there are different ways to cite the data there are two types of identifiers that you can use to search for data in your PMC first is DOI or digital object identifier DOI is bound to a URL a link indicating where the data set can be found in this example the author's have provided a DOI link in a figure legend and it links to an open-access version of a figure in a figshare repository second type is accession numbers accession numbers are another type of unique identifiers given to a data record to track it in a single database so each database will have its own set of accession numbers for each of the records that they hold in our second example the mass spectrometry data described in the publication was deposited to proteome exchange and assigned a number p XD 0 0 7 9 5 6 if you search program exchange for that number you will find that particular mass spectrometry result papers with either accession numbers or duis can be found on your PMC using already familiar advanced search page on the advanced search page please select data links and data citations section if you look at the drop down menu you can see which options are available to you in this case citations are first 2 accession number while data DOI citation is a whole separate option you can find all papers citing clinical trials or all papers citing a protein structure if you combine such search with other criteria that we tried out today you can find which publication on ulcers have a link to clinical trials which articles on arab adopts as' provide associated MOSFET data or which papers provide both structural and functional information for protein domains if you look closely you will notice among these options a different kind of data citation which is kind of reverse of the situation we just saw these are references to the literature which are added when the database record is submitted or curated so you shouldn't confuse these two what you would need is the citation the data citation in the articles finally and this is the last tip that I'm going to share with you today you can search for a specific data set like wheat genome or ATP a structure and to do so you would need to know syntax a specific command if you wish that you would type into your search before the keyword this is really only necessary for those of you who want to do very specific very advanced searches you can find the syntax on pmc help pages and it covers all kinds of search scenarios even if you want to find a paper that has been cited exactly 100 times the syntax for searching for a specific data set can be found by the link on the slide that goes to the syntax for database citations we can send it to you as well and here you can see that if you use accession underscore ID you will find articles with that particular accession number here's how it works in practice you type your accession number of interest with the proper syntax and you find one result that actually sucks that accession number if you don't use syntax and instead just type the accession number alone you get thirty three results most of which are not related to that set of data so that finally concludes our presentation we have covered different ways to define your search filters sorting options advanced search options author searches using orchid and searches for data cited in an article with DUI or accession number lastly let me show you how to get help and where to find further information on these topics if you need it I have already mentioned Europe BMC help pages they're quite comprehensive but if you're stuck in any way and you would like to get a helpful hint you can contact us by the email we have an active help and support team that is ready to reply to all your queries you can also follow us on Twitter if you would like to get notifications about new features or upcoming webinars there is also a list of upcoming webinars from the EBI if you would like to learn more and with this we're ready to take questions and we will also be very happy if you provide us with feedback about this webinar once we're done so if you have any questions feel free to post them in the chat box and I'll see what we have and try to reply alright we have quite a number of questions Christopher says would be good to update the patent indexing thank you for your suggestion I'll bring it back to the team Claudia is asking if it's possible to access the rare terms list for the relevant sorting so the way that the rare terms is defined is the system looks for that particular term across all articles and it counts the number of times that they're found in all of these papers so for each term there will be a score of how many times it is found so there's no particular list that you can see in terms of content coverage how much does your PMC have relative to other resources from the feek so as I mentioned your PMC covers all of PubMed abstracts almost all of PMC full-text with few exceptions and some additional sources such as a great Cola database and Chinese biological abstracts if you want to see the full list I will I can send you a link later on or you can find it in the help documentation from your at PMC a question from anvita is it possible to find population specific studies though it isn't mentioned in the title it probably depends on what kind of studies you're looking for so as long as you define your query you can do that if there is a specific database that hosts population studies and we have links to it then you can try to configure data search to do that task and can be directly download citation from the search results yes I have not shown that so I can show to you how it works now let's go to p53 mutation damage and you can export a particular search result so you'll select a citation and export it and then you can use it for exporting to your reference manager or copying it to any kind of table next are their sequence database accession numbers our sequence database accession numbers synchronized between PMC and Europe PMC from Christopher I am Not sure I would come back to you on that the question from gamma if the help desk is only available for European nations no just like the content is worldwide the help desk supports anyone who comes with questions so feel free to email us we'll be happy to help you out a question from Jennifer can you confirm that the biggest difference between PubMed and Europe PMC is that your PMC searches full-text not just the abstract in terms of search this is perhaps one of the biggest differences so Europe PMC will search through the abstracts and it will also search the entire full-text so for papers where we have the full text we will search through it for papers we're only an abstract is available we will search through abstracts there are other differences that I've mentioned in terms of content and features but in terms of search that this is perhaps the most important one a question from Ola inca can I access the website from a different location yes the website is available to everyone no matter where you search from a suggestion from Christopher whether we can add a PubMed direct link thank you I'll bring that back to the team and question from Claudia does the full text definition include supplementary materials in terms of search as far as I'm aware search doesn't go through supplementary material but if you use section search you can force it to search through supplemental files that will of course be only available for papers where we do have full text yes so a note from Christopher for the record if you query NCBI website it returns both abstract and PMC text matches that is true so you there is a way to do that just so that you're aware if you search on your at PMC you search both abstract and full-text with clinical trials it is similar like so there's a question from gamal if there is a section specific on clinical trials so if you want to find all papers with clinical trial citation you can do that from the data search like I showed you on the advanced search page if you have a specific clinical trial in mind then you can do that with the accession type search you just need to know the number that the clinical trial is referred by and you use accession underscore ID to search for such for that particular trial all right a question from Gamal so we can relate it to clinical trials gov I think that I'm I would have to double check which clinical trials registry we actually synchronize with I come back to you on that I'm not sure if that includes clinical trials that go Claudia asks about the API options there are already webinars available on your TMC API we can send you the link and yes we are planning more webinars and training on the programmatic access to your PMC okay if there are any more questions please post them now otherwise we will be happy to take any questions later on you can always email us if you have any more queries okay on that note if there are no more questions thank you all so much for attending the webinar it was great to have you and stay tuned for the webinar recording okay thank you take care and bye bye

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