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PubMed Search: How to get Optimum Results?

Feb 15 | 2:00 PM

Performing an accurate literature search is of paramount importance to keep abreast with the ever evolving medical literature. Literature search essentially implies finding answers to a specific set of queries. It involves application of “keywords” leading to the identification and retrieval of published papers from readily available electronic databases. However, one must remember that most of the scientific databases are not as intuitive as the Google search engine and hence, do not always yield the desired search results. This can be frustrating to a novice who is unaware of the different strategies that can be applied to refine the search. Join us for this engaging discussion and make your thesis journey a breeze.

[Music] so netflix welcomes you to this session on how to optimize your pubmed search results today we have with us dr sachi sane gupta he's a consultant ophthalmologist and retina surgeon he's also the lead medical writer and biostatistic statistician at sengupta's research academy he has a proven track record in clinical research with nearly 100 peer-root publications he has created the same gupta research academy as a research and publication assistant to ophthalmologist optomes optometrist and ophthalmopharmas very very warm good evening to everyone attending this meeting and you know i hope you'll be able to sort of make sense of pubmed which is a very large you know database of all the articles which are published on a daily basis so you know i think that this word optimize or optimum uh you know something which uh you know you keep hearing all the time not only with uh you know medicine but all over the place so but you know i think commit is one tool which really requires optimization and you know if you can use it in the best way uh you know your sort of results are going to be completely different like i said you know we need to really understand how to optimize and you know there are so many other things that you can do with pubmed in addition to uh you know just search so you know that's what we look at now in terms of how you can optimize your search and then what what more can you do with pubmed and you will realize that there is a lot more that you can really do with government and it is almost that you it will almost act as your own personal personal assistant in many ways if you are keen on doing publications so the quick outline uh is that you know we'll initially learn about you know what is midline what is pubmed and what is pubmed central or pmc and what are some of the differences between these because you know there are slide there these are slightly different from each other and once you know where all this is coming from you know you will be able to apply them better then we'll of course look at search strategies and uh you know how do you uh use something called the advanced search option uh and i'll show you some examples of how you can do it in the best way then you know what more you can do is you can actually create a my ncbi account and you know you can really get the best out of pubmed and get pubmed working for you and then we'll conclude and we'll summarize everything that we've learned okay i think the first thing you know before even we start is something that you can do on your own is you can go to youtube like we do on a daily basis and you can go to the national library of medicine's youtube page so this is the network of the national library of medicine or nnlm you can just search this and there are about two and a half thousand subscribers you should subscribe subscribe to this page and you know a lot of the material that you're gonna see here is can also be found on that page so please go to the nnlm youtube page and you know subscribe to this so that and you know you can also watch a lot of relevant videos uh there as well so you know this is one screenshot from one of the videos which is a teaching uh sort of seminar of our 46 minutes on you know what works and how commit works at the back end then you know a lot of good information is there on that video so you know there is something called pubmed tutorials which is available right on the pubmed website uh you know so this is the pubmed website you can if you scroll down you will see this something called the mesh or mesh just click on that and it will actually take you to the we go to what this is uh you know so this is the mesh page uh but then uh you know you go there on the left you click this tutorials and then this will actually take you to the pubmed online training web web page you know this has a lot of good material where you can actually learn and if you see these are two minutes four minutes videos they're really short videos there are of course longer videos as well which you can learn from too right so uh this is a really useful tool that i think you know especially when you're budding and you're learning these are larger videos of six you know about uh about 60 minutes and also there's one on 90 minutes so you know this is something that you should definitely explore and this is right there on the website but it's at the bottom of the page and you know sometimes it is actually missed so you know this is what uh the you know comment actually offers tutorials for you to learn as well so you should all make use of that uh you know so now coming to what is midline what is pubmed what is comment central and what are the subtle differences between these so the overall objective is you know by the end of this session you should be able to distinguish between what is medline and what is a non-medline record in pubmed because pubmed actually has something which is non-medline and i'll tell you about that and then you should be able to define mesh headings mesh to make the topics and mesh some headings you should be able to conduct a basic pubmed search and get relevant results you know so this is what you call uh you know this is what we are discussing today so optimizing means getting relevant results then you can manipulate the results display and see so many different things that i'll show you examples with then you can move from your pubmed results to other sources and then you can uh like i said you know identify how to customize pubmed and use your my ncbi account so what the first question is what is midline so the midline was established in 1964 it was a database of citations to biomedical journal articles right so this is what came together after major uh you know funding was approved by the uh you know by the us senate and then you know this came into existence in 1975 1964 and what really is is it is a database of citations you know so uh to publish biomedical journal articles and so this is a uh you know let's remember that this is not this does not have the entire article but it basically has enough um you know material from the article for you to understand what it is about and then it can actually send you to the original articles website and then you can actually try and read it but so it does not hold the entire articles it does some and i'll show you a little later but it really is so medline is a database of citations and this biomedical term is a very large umbrella under that you have of course medical articles you have uh you know biochemistry or chemistry related to medicine you have clinical psychology you have limited genetics so you have a lot of other heads under the biomedical journal umbrella and it has over 25 million citations going back to the mid-1940s and there are over 6 000 journals which are currently indexed in medline so when you look at a biomedical journal and you know it has many indexing uh listed on its website so you should look out for whether it's indexed with medline and then you know journals must be approved by a review committee because no you know any journal a freshly launched journal cannot get into midline and so we will see you know which journals can get into midline and then most citations are in english language articles and include abstracts now so who decides what journal should be in midline so there are quite strict uh you know criteria based on which they accept uh journals into the medline database this is decided by the literature selection and technical review committee so it is made up of medical experts and librarians they meet three times per year they consider approximately 180 titles at each meeting so imagine how many journals are applying to get pubmed indexing and they roughly select about 20 to 25 percent of the you know journals which have applied for it and the rest are actually rejected and they are asked to you know come back later with whatever modifications have been asked right so the technical selection uh i mean the literature selection and technical review committee does all this work at the back end and what criteria they really use is you know the scope and the coverage of the journal like i said it has to be bio medical related there are journals in engineering and so many others which are not uh you know eligible to get into medline then they use the quality of the content then they use the quality of the editorial work the production quality the you know audience that it is serving and then also the type of content that it is actually you know auditioning out so and most journals will require at least uh you know four issues every year that is very basic and then there are many other things like the editorial board and you know so this technical assessment committee goes into a lot of the basics of the journal and you know the journal should be in existence for at least two years after which you can apply so uh you know it's quite stringent and difficult to get into midline so that's why you know if a journal is indexed in medline it has to be of quite high quality otherwise you know it will not get into midline so if you are reading a journal which is not indexed in medline that means you know it has not satisfied some of these criteria and probably there are you know that something which can't be trusted as much as a journal or an article which is uh you know indexed in midline the next question is you know what is pubmed and is it really different from the medline so you know the pubmed is the front face of the medlines you know this is the website of the pubmed i'm sure most of you have taken a look at this you know so what permit really is is you know it is composed mainly of 90 of it is composed of medline right so there are certain articles which are in process and they are not yet uh you know not yet maybe they are published ahead of print by some journals and they're still in the process so they constitute about two percent of uh you know all articles involvement and then there are uh others so other records like book chapters or maybe books by certain publishers and many other uh you know such sort of communications are also uh it is also possible to get them indexed into pubmed so government really is the you know it is the larger uh you know sort of umbrella under which most of it is medline indexed but you know there are certain others so pubmed has a larger uh you know sort of coverage compared to midline alone and you know it's a very large database like i said and therefore a lot of people use this more than two million users on a daily basis uh that's 20 lakh uses on a daily basis about 5.6 million you know views are uh ours you know articles has seen about 5.2 million utilities are api searches so apis are basically third-party searches which are using uh you know medline services and then there are more than 2 lakh users on mobile devices in addition to the two million which are on the you know website so uh you can see a very large volume passes through this website on a daily basis and now what is pubmed central you know so like i said you know medline and pubmed basically have articles in terms of the authors the you know the journal and the abstract they don't have the whole article however you know if that whole article is made free by the publisher or by the author or by some others like funded by the us government then those articles are available free to be read so what they are done is they are actually included in pubmed under the heading of pubmed central so what it really means is all free full text articles you know so the sort of working your word is free so all free full text articles are archived in pubmed central right so uh you know essentially if pubmed has about 33 million citations of which about 7.3 million are full text and free so they are part of permanent century you can see it's about one-fifth of all the articles in common are actually free and available for you to read so you know i'll show you examples of how we can you can access this uh slightly later and so we started out with looking at uh you know what is midline and what is pubmed and what is pmc so now you know slide differences so pubmed is the larger umbrella under which medline and certain others like books and in process articles are there and permit central actually contains the whole article and it is available free to you once you know these differences then we look at certain search strategies and you know how you can uh you know optimize your uh your searches so this is the pubmed box and what i have put inside that is is quite interesting and it was you know we have also used this uh as an introduction to the course so you know this uh this search box is not really as intuitive as the google search box and you can really throw anything at the google search box and you know it throws back a lot of relevant information but then a lot of the times you will see they are repeated so the first three or four may be from the same uh you know maybe from the same original source so google doesn't differentiate those but you know you can't really do that when you're looking at uh formal medical data so permit.jov or this this box that you will see is not as intuitive as the google and really it is based on keywords you know the most important part is keywords if you feed it the wrong keywords you will get the wrong results if you feed the right keywords you will get the right results if one if something is if you know one thing that you want to take home with you today it is keywords so think hard about all the keywords that you want to put and you know if you put relevant keywords then you will get relevant searches and most of these keywords should be fitting the mesh terms we'll look at that in a minute and then you know this also uses uh automated term mapping and i will take a look at this as well you know so ah if you are using if you are not using the right keywords uh you know comment stills tries and matches those to the keyword at the back end so that is called automated term mapping that's why the word automated you know so what are these mesh terms so mesh healing is a mnemonic for medical some subject headings and is the nlm controlled vocabulary thesaurus used for indexing articles for pubmed right so as you can see you know this you can see like a tree and so mesh terms are really like a tree once you see examples you'll realize that you know how these can actually impact your searches so you know where you will see mesh terms is you know when you look at you know this is one of my articles which is published about a couple of years back you know so on the top of it you can see you know factors affecting treatment outcomes in uh congenital nasal electromagnetic obstruction ah you know so the immediately below that so this is called the abstract page and immediately below that ah is you know the purpose methods results and other things if you keep scrolling down you will see something called mesh terms and i'll show you examples uh again later on so these are called mesh terms here so these are as close to keywords as possible right so mesh means medical subject headings these are added by uh nlm indexers you know so whenever an article is coming uh there are people actually sitting in the back end and trying to pick out important keywords from that article from you know from the message that is being given out by the article and you know how it can match better when somebody's searching for similar articles and what they're trying to do is you know they are trying to uh convert all the keywords into uh mesh terms right so that is what mesh really means again like i said you need not really see absolute details on this you know so this video will really show you what mesh terms are you know so where you get to mesh terms is by scrolling on the pubmed home page and then clicking that mesh terms and at the bottom this is the mesh terms you know say you search cancer yeah you know so what is the mesh term for cancer as you see it is neoplasms it may not be very clear to you but that is neoplasm you know so there are many others but then cancers are not if you search uh something with cancer then you know what is going on at the back end is neoplasm the next thing you know it's i've put cataract that's my speciality so if you see something like that you know cataract is actually a keyword which is great then cataract extraction is another key word to try and use you know the best keywords i've given some more examples uh you know say let's say i've put pancreatitis okay so if you see pancreatitis let me zoom in you know so pancreatitis is basically there as a keyword if you see below that pancreatitis graft acute country that is chronic pancreatitis alcoholic these are all important mesh terms uh you know say i put one more say diabetes and so once you put diabetes uh you know so the key word is or the mesh term is actually diabetes mellitus then diabetes insipidus now so when you are searching for something for diabetes it is advisable to use the whole word that is diabetes mellitus instead of using diabetes alone right so you know another example say you go to cancer so what this is showing is that this is the main topic and when you click that then you will see these subheadings you know so there are plenty of subheadings there abnormalities analysis you know there are many others so you can actually click on any of these and you know get relevant keywords when you're looking for something which is more specific right so you know these are all the keyword or sub headings you know so the main heading and the sub heading if you scroll down you know you will see all these uh main headings there so tumor neoplasm etc uh you know and then when you you know go by below you will see these are sub headings you know the cyst assisted the many different types of cysts which are you know described in cancer and if you scroll down you know so these are uh many different types of uh you know histologic neoplasms then where a lot of the leukemia the lying then ah you know neoplasm by sight then uh you know all these are examples of uh you know how this is constituted right so uh this is basically how you will this is just example of breast neoplasm again you know you go down there and this is how the trees you know so this is the main disease then you have the main category and then you have the subheadings so these are all examples of you know say suppose you want to search something which is specific for breast cancer then you can actually click one of these and see what is the actual mesh term which is ah you know for that particular tumor yes okay so these were some examples of how you can use this mesh terminal the idea is to use the exact keyword that pubmed wants uh you know so like i said it is not as intuitive suppose you are not using the exact keywords but then using something which is very close you know say if you use cancer uh pubmed is going to understand that you are talking about neoplasms so the back end is neoplasm so it's going to automatically match that so that's called automated term mapping or atm how many useless automated mapping or atm which recognizes thousands of concepts and maps to an appropriate mesh term right like i gave you an example and what it really uses let's say for example you're looking for hiv aids you're looking for you know drugs and then breastfeeding uh you know so what is safe what is not safe and what it actually uses is you know same so the subject matter is going to be matched to the medical subject heading or the mesh term and then it is also looking for journal titles it is also looking for authors so you know so if you type an author's name you want to search by author you know if you have slightly wrong name maybe one or two letters then you should probably still recognize that you are looking for you know that author again you can search with the journal titles uh you know so that is basically also something that you can do just a second i'm not sure this is a video okay so uh so this is not a video you know so uh what these keywords like i said you know the search will be relevant and optimized only if you use the right keywords and the keywords like i said you can search from mesh terms you know sometimes you may not get any output at all from pubmed so uh you know probably your keywords are not in the right place so you can search for you can go on the mesh term and look at what is the exact keyword and then conduct your search if not automated term mapping usually helps ah you know so after this you know is there any other way that you can uh you know optimize pubmed to get better results and that is something that you should uh know uh the answer is uh you know is right below that box that's called advanced search option you know so once you look at the advanced search option uh once you click on that advanced search option you know this is what you actually see uh you know where it shows all fields and uh you know all of these so this is the actual page that comes up when you click that uh that advanced option you know so you see all fields you know so when you go there and so you click that advanced option and you know when you go there these all fields are there when you click that and you will see a lot of options which are available you know you can just leave it uh just like that as well but you can actually say author you can say mesh term or mesh subheading or journal name or whatever you want to but it's usually better to keep it you know just the way it is uh and not so you can see all fields and then these are and add with and add with not or add with not or add with or okay so these are the three things which are there on the right you know so if you look at that right box it will say you know so if you look at this box it will say uh add you know add with and or or not right so okay so i think it will be yes so this is the actual page that you will see like i said you know i've shown you once what happens when you use that drop down it is better to use all fields instead of actually adding something specific and you know then what is this add not an or that is something that we are going to see once again yeah now so this basically helps us put all the words together so these are called boolean operators uh or boolean terms you know so and means when you see the examples you will get a better idea but and means uh you know both the terms are part of your search should be part of your search you know say for example incidence and the name of the disease you know both of them should be part of the uh output that you are getting the second is called or uh where you know that first keyword and the second keyword either or can be there or so one or two or both can be there in the search the third is not where only one term should be there and the other should not be there let's say for example you're looking at you know outcomes of breast cancer surgery and you don't want outcomes of say stage four breast cancer you really want to see you know so your term will be you know cancer and then surgery and then it should not have stage four right so look at this uh you know it might be called advanced breast cancer or whatever if you look at the mesh term you will realize what that term is so you don't want outcomes from certain parts of the disease so you can actually exclude that right so when you use these boolean operators clearly you know you will get good results generally we use this and you know to get good results so this is basically putting these uh these terms together so i'll just give you an example you go to this advanced search you know and uh you know you can say i want to see you know what are the articles and end up thermite is uh i just you know before this you know what we are looking for as an example is to look at the incidence of post-operative endophthalmitis in india you know so that is uh you know an infection which happens after cataract operations and is quite devastating so we want to see the incidence of post-operative endophthalmitis in india you know so we'll see how to constitute that and how to actually optimize and narrow down your search and so you go to the advanced option and then you say endothelmite is and that is your main keyword and just you say add and you click on search and what happens is you know all this comes out so you will see about 11 000 articles it's almost impossible to go through all of them and so what you want to now do is uh other thing you can do is you know you can sort that by best match so you know you can have a summary or abstract or pubmed so it is always better to have that summary mode and you know the best match mode on you know so that you will see the best match uh it's also possible to have uh you know most recent and others so out of 11 000 articles it's all possible to look at all right so you can go back to advanced option and you can go below you know your searches will be saved there so you just add that query you see and document system on its own then you say uh you know in india you know so that's what you want to do if you're trying to narrow down your search and once you say search if you say that you know there is and in between it has come down to 760 articles right so this is relatively more manageable but still you want to do more this is one of my papers which is actually not first and i'm quite happy with that you know so it shows that summary view again you know so we want to bring it down more so what we do is we you know say add query again and then you know we say post operative that's because there are many types of end of this matrix so you need to have some subject knowledge there again and is being used you search it down you know it comes down to 281 articles now because it's uh considerably lower still we want to now only know incidents there are outcomes and there are so many surgeries is that but we only want to know incidents we just type incidence and when you say and and you search and you're now looking at 85 articles that's significantly slower than 11 000 that you started with okay so you know you can actually try and uh you know it may be getting pixelated you can also you know on the left panel there are many uh refining uh modalities again you know so what we've done is you know looked at only from 2000 to 2022. there are now 81 articles you know maybe the older ones are irrelevant now now you can then scroll down and you can again you know filter it by free full text only free full text i want to see so that has come down to 36 articles now okay so you can just sort of you know optimize your results by using all of these options let's say you want to see only for review articles you know you really want to learn say for an exam you are studying so you only want review articles there are 11 articles in that now you know that's relatively more manageable right so uh something like that you can just scroll and you know i want publications from only one year last one year the most latest papers i only want to see those you know so you will see again that is only 11 articles right so in one year there have been you can clear those all and then you will see again 85 results you know there so there are you know so how you have seen how we have come down from uh you know from uh 85 from almost eleven thousand articles on overall on endothelius to uh you know on uh we've come down to and you know sort of optimize it to 85 articles okay then what happens is when you click on one of the articles you will see something called the abstract page okay so let me try and show you that uh now so what we are looking at is search strategies you know in search strategy we have also looked at advanced search options and how to actually you know get to the right papers that you want to do now what happens if you click on one of those papers you know what will you actually see in that that is called the abstract page okay you know so this is what we've already looked at we looked at what is medline pubmed and government central and then we've looked at you know all the different search strategies so use you know the keywords using mesh terms and the atm as well as using that one search option now you know we'll again see so this is another video so you know this is the end of the mites and india you know so there are 760. you click one of these as soon as you click that what is this is called the abstract page and so this has a lot of information too you know on the left it says review right so this is a review article then this gives you this this is the indian journal ophthalmology and it's published in 2017 you know so then the name of the journal then the name of the paper then the authors and you can actually expand and see which institutions they are from uh you know so all this information is also available you know then what is available is the pm id number that's a unique number for each article which is published in pubmed uh and the doi is also available on that same page which is useful then you know you go below and actually get the gist of what the paper is about you know so this purpose methods results and discussion uh when on the right you see this is the full you know full text links if you see there is pmc free full text you know so that means this article is free to read and you can actually get the full text and sometimes you know it may not be free but then it will lead you to the journal website where you can actually read sometimes you will be surprised to see it's free and this is what happens when you pick the site so if you want to cite it uh you can do that as well on the right panel you will see uh you know all these shortcuts where you know title and authors abstract conflicts of interest similar articles and these are cited by these are all at the you know if you scroll down you will see all of these but to go there quickly you can just click these you know conflict of interest in is nil there are uh you know similar articles which have also been shown there uh you know just to help you get better results then these have been cited by 13 papers which is also a great number then all the references which have been used in this uh article uh there are 42 references you can get a list of all of those as well you know so this is what you look at you know you see when you look at the abstract page of you know any paper so you know something that you should remember is you know you can go down to any of these sections if you want to and on the on the top right is what you will see the links for the pmc or the you know comment central free uh you know articles so you can get the full text without without any pain and remember that almost twenty percent of articles are you know freely available so which is which is a great thing right so you know this is what we were trying to see so you know what we have already now looked at is how to actually get the best search right now how you can use or what more can you do so you know what you can really do is you can customize comment by using the my ncbi account and i will show you how you can do that uh it really allows you to save searches or save records in forms of collections or sometimes your own bibliography uh you know you can customize it in many different ways let me give you quick examples of those now so on the website you must all make this my ncbi account even if you are very young or you're old it does not uh you know it does not matter so so when you go on the abstract page you know all the information that is there is all self-explanatory you know so you see the name of the author the name of the journal then the title of the paper then you actually have the abstract of the paper in the purpose methods the results and the discussion or the conclusion and then you should also scroll more so you will see more things most of the times you know we just see that because on the page you just see real conclusions but most of us don't scroll more but you should scroll more below you will see similar articles because you know remember they are all showing you output from search from mesh terminology so scroll below and then you'll also see the actual mesh terms which have been used for that article and you can use the same mesh terms for you know sort of modifying your search or getting better results from that so uh you know this that's basically what you will see on the uh abstract page uh you know then when you like i said we you know we are trying to optimize uh pubmed in terms of making it work for you so this is all free so you should go and log in and you can log in using your google facebook and all these ids right once you click login and you can actually it's very simple you can log in this is the page that you will see right so uh you know on the bottom left you will see it's called my bibliography and then on the right it says saved searches uh you know there are these are some of my saved searches that you are seeing there and then on the bottom right you are seeing some collections there so how do you save searches you know what can you do with safe searches or something okay so i'll just go to the video okay you know so i'm just still using the you know 85 uh results from that end of telematics in india you go and you say create alerts and then you can name the search say you know whatever end of in india uh you know you can just name whatever you wanted dash incidents and then you know that search terms don't touch that and you say you would you like to get updates on you know similar search results and you can say i want weekly updates or you know you can say monthly updates then you can choose which day you actually want it to be and so i have just said saturday and you want that summary uh you can just choose whichever day you want to right uh then you can save you know this is the summary view i want and then i want 10 items and just say save and once you say save that whole search has actually gotten saved now where you will see it is you go to your account and go to your dashboard on the right you know that's where on the top uh you know you can see this end of thermitis in india this is the saved searches uh you know and when you uh click that end of thermitis in india you will actually see that same page so your searches actually have been saved isn't it this can only be done if you have a my ncbi account right so this is an example of uh saved searches i think there is one more video here so these are you know this is the same page the other thing on the bottom right is looking at collections right so i'm going to try and show you how to make uh collections uh okay let's click because the video is a little far away yeah you know so you know now know how to save certain you know say you're doing a thesis topic on this is for something that you want to keep in touch with you know say for example i want to keep in touch with diabetic retinopathy and you know certain advances in that very specific domain so that's what i will do i will say you know whatever is released or whatever is published in pubmed on this particular disease and this niche entity of the disease i want you to send it to me every say saturday or something you know so and if you come to your email inbox and you're saying my ncbi and when you click that in you will see all these five or ten abstracts which are there you can click you can go to the full text if you want you can read because how do you really keep in touch with literature or you know what is new uh you know what is happening in a particular disease uh you know you can actually do that uh you know if you say you know poverty 19 broadly you will get like you know say 1000 articles published every week but then you know if you say very specifically about overweight 19 and you know this and this or this or or you can say not so use those booleans or just make the search very specific then all these you know reminders that are coming are also going to be that specific right so you know remember that all of this base is based on the uh search terminology or the mesh term that you're going to use right so the other thing is on the bottom right you're seeing these are collections uh you know so in addition yeah so in addition to saved searches what you can do is actually make collections so when you go to that uh you know that instead of saying create alert you can go on the bottom and say send to right and then once you go to center you see it says clipboard or mybibliography or collections or citation manager you know when you click collections uh you know this is what it says you know add to collections and you know all results on this page it will you know once you click you will see either only those results on the page that is those 10 uh results or all the results you know so that and then you can say add to existing collection or you can actually create a new collection and then you once you do that and you say add it will be added to the bottom right of your you know dashboard uh bibliography like this on the bottom right you know so i have some favorites i have my bibliography and all of those right so suppose there is an article that you have published yourself you know when you look at that abstract you can just say send to my bibliography and that's it you know so your publication list is actually getting populated uh as and when it is coming up so you know this is what we started out with where uh you know midline differences between medline pubmed and pubmed central so remember pmc is all free texts uh which are full text which are free then there are search strategies uh especially using the right keywords using the mesh terminologies and the atm as well as advanced search options to you know narrow down or define your results uh then you can create your my ncbi account and you know get pubmed to do the work for you you know so overall like i said you know these using mesh towns is really important as in when you start searching you will realize that either you are getting irrelevant searches or you are getting too many outputs so you can start refining them uh be mindful that it is using that atm at the background you know so if you are using something which does not exist at all in their mesh tones you are going to get zero outputs right so mindful that it is using it is trying to understand you using atm but it's better that you use mesh terminologies uh then you know try and refine if you're getting too many outputs then try and use the advanced so sort of the echo messages if you are getting too little output or you're not getting anything that means you're not using the right uh keyword so look at mesh tones and get to get to the bottom of that if you are getting too many outputs or if you're getting too many uh results then you need to refine it using advanced search options and the you know this boolean operator is the one that you use uh then like i said you can customize pubmed uh to save your searches make collections uh your own bibliography as and when it gets created you can create alerts you can explore more on on the website so these are basically how you can use permit and optimize to the best way you know this is my website uh i think the introduction has already said this is independent academy and there are many blogs interesting blogs which you can read on how to read a scientific paper and you know many others like sample size calculation and thesis to journal articles etc what is open access dr kulkarni is asking yeah i think that's a great question and you know it's probably another session that we should join around something like that there are two ways of where you know where a readership can consume you know what is being published one is by paying for that paper uh and you and then you can actually read the paper but the second thing is where you don't pay anything you just go to the website and oh wow wait it's all free but remember that you know there is somebody who is actually paying for the whole thing you know so there is no free thread here isn't it so so there are two ways of looking at this open access means the readership does not pay but the author actually pays something called you know manuscript processing charges and it can really extremely you know from say rupees 3 000 to something like 3 000 us dollars so that's a huge difference way is not open access the author does not pay anything but the readership is right because there are a lot of costs etc so open access means the readership gets everything open access or free that's why then open access uh the other is it's not really closed access but uh you know somebody is paying for that subscription fee so if you're an author you know it's easier to publish in journals which are not asking you anything but then they are asking the readership routine only thing is that you know your leadership will not be that large isn't it or it may take time for your growth open access journals typically have very large leaderships as soon as they publish 10 12 000 people will read it so you have a large audience base who will read but then you know you'll have to shell out a lot of capital foreign access journals include something called creating journals you know where they actually charge money from you but then you know it is you know entire process is completely shady it is not indexed in pubmed and you know like i said uh you know we should have another session on what is open access you know what is the credibility of the journal so if you're looking at an open access journal even if you're reading or you're submitting as an author first try and eliminate that being a predatory journal once it's not appreciated because there are a lot of open access journals which are very good they're all you know one easy way to look at it is this indexing red line if this journal is indexed in midline like i already showed you there are a lot of stringent criteria even if it's open access if it is interesting when you're looking at something which is high quality but if it is not indexed in midline then you really have to ask yourself a lot of questions which can we can discuss another session if you wish but uh you know so open access journals may not uh always be through youtube must try and that is a caveat that you should remember i think i i hope that answers yes dr pruthway is asking in one of your slides there is a search phrase with lot of open and close brackets does it have any relevance so you should remember that it's better that you don't use brackets yourself so the brackets are being made by the atm which is working at the back end so what you can really do is use the booleans you can say add or or not and then those brackets will be put by the search engine itself and that is a better way to go so don't put any punctuation marks you know commas there are many ways of doing this uh you know you can put brackets you can put inverted commas there are many other ways to do it but i would suggest that that is at the beginning don't use any punctuation marks and you know let the search engine take care of itself uh so if you use any punctuation marks say brackets don't use any punctuation marks let the system do that for you you know you are already using advanced search that's the whole idea of using that advanced search uh well these were the questions from the reader's point of view one question we have is from publishing point of view like dr anjali wants to ask that how to publish like what are the good index journals and the where they should apply if they want to publish yeah so one is the nlm catalog so i did not speak too much about you know this much time not enough to keep your attention as well as you know keep showing you more about pubmed so problem is something called the nlm catalog where all these six seven thousand journals which are there are all uh there you can you know sort of you know see them in terms of the subspecialty you can see them in terms of alphabetical order and all of that right so uh you can use the nlm catalog and look at some of the journals now how to choose index journals is something which we should also have another lecture on how to actually choose a journal of choice where you know you ask a lot of questions in terms of is this permanent indexed is this uh you know we have reviewed so what is this peer review and other things and then you know is is your article fitting the scope of that journal so just naming two or three there are about at least eight or nine things that you should ask yourself before you choose a journal uh you know there are many uh websites which actually help you match so you just copy paste your abstract with the proper keywords well written and you go to scopus sorry i can show you some examples when we discuss these things so you know just copy paste your abstract and then just say search and you know that search engine it is ai based it will actually show you names of the journals which will be interested in the paper like yours based on your keywords and based on the scope of the journal and so many other things so then you know three or four you know this is something for somebody who is very new and nervous and not really sure what is happening but then you know these are you will really discover so many journals which you may never have heard about it so you know how to choose an index journal you know obviously if as soon as you talk about an index journal uh open access is rule i mean not open access your radiator is ruled out isn't it now whether you want to choose an open access or you want to choose it all depends on how much capital you have of course and there are so many other things and most journals which are still the very prestigious ones are not yet open access they do allow open access publishing as well but predominantly not open access right so how to choose a journal is something that you know we should also have uh you know my lecture series is there if you want you can actually take a look at that if you can if you want to enroll you can actually look at all of these quickly we can we will probably have sessions as well as ebola all right there's one raise and request dr surya kandoke i'm just accepting your request please turn on your audio and video dr surya khan can you hear me one question is uh yeah yeah by dr agarwal please comment on scopus yes you know so what we were discussing today is pubmed but then scopus is another uh database like government you know focus is predominantly run by elsevier who is a publisher and they have so many you know they have thousands and thousands of journals under their heading so scopus is essentially an index for uh it was being published by savior so elsewhere does not only publish biomedical articles they publish uh you know so many like uh you know say a lot of engineering based uh papers are published in scopus index journals and you know a lot of others like psychology where it's called qualitative research a lot of those kind of articles are published so purpose essentially is not only is not free to use uh scopus has uh you know has a subscription fee so but then you know as a focus on a lot of other things not just search they have you know links to if you have subscribed to scopus that hence you are a paying customer of elsevier then you have uh you know access to all the articles if you search and then you there is nothing like free not free you just go you access that a lot of universities actually place focus i mean pay and have a scopus you can look at your own citations you can you can have a lot of metrics saying you know your what is your own personal index um you know but then scopus is something that we would probably not use in daily uh there's another index like this called mbase that is even more predominantly engineering based so you know if you are looking at uh you know something which is like a medical device or something which is new and you know has this been used on animals before or you know is it toxic to the human tissue that is being done or something like that then you might actually try and look at mbas or scopus there is another engineering based uh thing which is called ieee so you can [Music] so authors can actually you know deposit their free text our full text articles onto research so it really isn't something which is you know regulated as much you know so you can upload uh your paper or you can upload a project you're working on or something like that you know so if somebody wants to know how many publications you have then they can straight up go to research gate and then look up your profile and then you need to keep updating that and it auto updates also if you have you know if you're linked with so the circuit is essentially uh you know i wouldn't say it is first to show off your publications but you know it essentially i mean in the beginning it really started like that but now it is part of the elsevier network so you know mentally is another software which you can use to uh you know make your reference list automated references so mendeley research gate all of these are now all linked together right so in research great the good thing is that you know you can of course if somebody asks how many publications do i have or you know is there a repository of all your papers that you work on you can just say oh i'll send you a link and so i would i would rather send a pubmed uh my bibliography link isn't it like i showed you you can do that but then you know if not if you have published many articles which is not in pubmed index journals then you can send a research greatly there are many other websites like that one is called problems problems can let you look at your articles it also allows you to uh you know document your peer review a number of articles that your peer review so clearly you act as an expert as a reviewer and then you are helping journals and your overall helping science improve so pub launch is one where research is another uh there you can also interact with other authors you can ask them questions and things like that but you know overall it's not really regulated as much so you know once you do google search now what you will see more is research grid on top you know because they're optimizing somehow at the back end where you know they are somehow showing up first but then try and look at those so my doubt is regarding nlm catalog so for example if i'm searching for an journal title which would be appropriate for my publication uh like once we put all the mesh terms out there and when when we get all the journal titles over there so there are certain things like currently indexed in my medline not currently indexed in medline so as far as my understanding i think medline is basically a subset of pubmed right most of the additional things which is about eight to ten percent these additional things are not journal articles they are book chapters and they are sometimes there are website links uh you know there are some which are in process and what that really means is that some journal now has applied for uh you know a pubmed indexing and it has been accepted but then it is still in process or there are some articles which have been published ahead of print they are not yet in pubmed but they are in process you know so they will still show that so pubmed will show it uh so that is essentially how you know so there is only minimum difference but for the catalog no if if you see that journal is not indexed in midline that means it isn't but then you know if it is part of the if it is throwing up that means you know they have at least applied for it you know so it they may have been rejected or not but sometimes you know at least it shows that you know the editors and you know they are at least aware that they have to get it i don't know whether that answers your question but uh the main thing is that if uh for example it is currently indexed in medline it also means that it is indexed in pubmed and also if it is not currently indexed in medline does it mean that it's not part of pubmed or it is a part of pubmed so those sentences the first sentence is entirely true if it is you know if it is indexed in medline that means it has to be under problem but then if it is not indexed in midline it could still be in permit but the chances are one out of ten so then you know sort of a blanket statement it is not index in midline uh you know it's probably not because we are talking about journals right if you're talking about one article somewhere here and there it is possible that you know it is an information but not in midline but ninety percent of the time that is not true if it is in midline that means uh dr kalpana is asking if anyone wants to see their articles impact factor how to check that so you know two important concepts here first the impact factor relates to uh you know journals journals have impact factors authors don't have impact factors authors have something called the h index essentially what you are i think question is you want to see how many times your article has been cited you know so that means how many papers which have published after you have actually used your article as a reference in their articles so that really means citation so that is very easy you can just look at your article and comment and scroll down it will say you know like i showed you one of my articles published two years back it has been cited 13 times this is good enough you will be able to see uh you know that and then you can also go to your article and you can say later you know it's just one it may not have been the whole 85 list in just even one article you can as soon as the article is published you can go to a problem and open that article and just say create alert and you know you can save daily also if you want you can say once in a week like i already showed you and you know as soon as it is cited by somebody else in a in a pubmed index channel you will get an alert you'll get an email that your article has been cited right so how many times your article is cited really shows the actual value of your article now journals have impact factors you know we should have another session on entire session on what are the impact factors and then authors have some called each index and then that also merits another session but then essentially what this means is you know say i so for me each index is 18 that means i have at least 18 articles which have been cited at least 18 times you know it's a big thing to have each indexes in double double digits and almost nobody has each index of triple digits that means you have at least 100 papers which have been cited 100 times which is almost you know it's very difficult to do so you know the age index really shows how much impact your work is having so i think that that explains your question yes uh well those were the questions sir so thank you so much and like we said right now that we have many more topics which would require another session just a q a session won't suffice them so i would say thank you so much for this informative session and thank you to the audience as well

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dr. Sabyasachi Sengupta

Dr. Sabyasachi Sengupta

A Consultant Ophthalmologist & Retina Surgeon, Dr. Sengupta is an phenomenal teacher and loves to make the concepts of research, publication and statistics easy enough for all medicos and thereby insp...

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dr. Sabyasachi Sengupta

Dr. Sabyasachi Sengupta

A Consultant Ophthalmologist & Retina Surgeon...

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