 So we're going to start with backlink in a general sense and then we'll move specifically to backlink in Vitek I'll start with that because it's relative. It's important. It's relatively clear We start with this we go to this we go to this and we finish After that we'll get back to our sum of discussion of reports Okay, great. So for the first thing that the most important thing about backlink Isn't the backlink software step number one is not backlink step number one is get your data file So the purpose of backlink is to convert existing data Okay, I can you hear me I already start I am starting yeah Okay, okay, great. So so In the purpose of backlink is to convert existing data So in order for backlink to work, you need to have some data first If your data are in Excel or access or somebody's giving you data, you're already done You already have that first step you have a data file But if you have a machine like a Vitek or Phoenix or a micro skin Or you have a lab information system like Polytech or Cerner or Sun Quest If you already have some repository step number one is not backlink step number one is to get the data out of your system To extract the data to export the data from your system. So I'm going to go to This PC in my upper left-hand corner. It says this PC. I simply want to open up my computer's files And here you see my folder the C drive and here you see a folder called who net I'm simply entering the who net Documents folder so I've gone to windows who net documents and Here I have a lot of folders a lot of files The top half you see all of these backlink tutorials the bottom half you see all the who net tutorials So let's see. I'm going to start With this one here called backlink AST by tech to in fact, I think these two are both the same document Yeah, English and yeah, we removed the word English. So I'm going to go to that first one backlink AST by tech to This document was originally prepared in Spain. I'm sorry in Argentina And it was in Spanish and we I did a quick translation into English the formatting is not great formatting is fine But we do want to that's why this one says the word English because it did not start off life in English So so step number one is how do we get the data out of a vi tech? so The vi tech software so what you see here on the screen is the vi tech software the vi tech to software So any of you familiar with the vi tech when you turn on your vi tech, this is what you see you see six big icons The one in the lower right-hand corner. I'm going to zoom in is Called the toolbox and you can see it as tools in it So you would click on the toolbox and you see a few options on my screen you see four options You see that second option is highlighted. It's called export inactive isolates. That is the key menu option One of the nice things about starting with vi tech is that it's the simplest of all possible exports It's so easy to export the data. So it makes it a nice way to start on top of that It's also extremely common which also makes it important You click on your toolbox you see the option called export inactive isolates One comment about that I would say this option exists Activated on about 98% of the vi techs that I have seen So not a problem you can do this Sometimes you do see the option called export inactive isolates, but it has been deactivated disabled It's disabled for one of two reasons one is it has not been installed by the vendor And that's usually not a problem just call the vendor and so far the few times this has come up Like all the vendor the vendor comes over in a day or two and install the feature So I have not yet seen an example where people have to pay for this feature extra The vendor people said yeah, I installed your system. I didn't think you needed it So I didn't install it. So if you see this feature, but it's grayed out One reason is that it's not installed called the vendor and hopefully they'll just install it easily and quickly for free There's one reason the menu option might not be highlighted activated The second reason is that maybe you're logged in as a technician and you need to be logged in as an administrator So sometimes you simply need to log out As a normal lab person and log back in as a lab supervisor or lab administrator So but that's a rare situation 98% of the time the feature is there the feature is activated for everybody So when you click on that option called exporting active isolates that will bring you to this screen Uh, let me just move that red. I don't know where the red is over there, but But let me just leave that red that doesn't help. Okay. So this is what the export screen looks like In the lower left in the left side of the screen. All you have to do is a few things Click on the start date and the end date so you can export from january 1st to january 31st January 1st to december 31st. Just choose your time period I was a little confused by the vitak at ephi because I tried to export the 2019 data and the number of isolates was zero I said, how can it be zero? You've been entering data and then they explained to me that Yes, we have data from 2019 But we are lying to the vitak The 2019 data we are not calling samples from 2019 Why because their computer Their vitak panels are expired were expired And the vitak the vitak will refuse to use I'm trying to move my screen around a little bit Well, okay, that's not working I have my go-to meeting control so in the lower right hand portion of the screen you see the date and today's date is 2020 But on the vitak at ephi, I noticed the date was a different date Because they were tricking the system they had panels. I don't know from 2018 So they had manually changed the date on the computer to 2014 maybe In order to trick the system And so then the panels would work So when I tried to export the data from 2014 to present it worked fine It's just a funny thing that they had changed the date. So that's a funny thing about that that system Okay, hopefully they're back to normal panels now and hopefully they could put the correct dates So step number one just choose the start date and the end date Uh, keep in mind. This is not the sample date. It's actually the test date And the test date is an autumn is automatically generated by the date on the computer So if you test it on 2019 it'll say 2019 That's step one step two is you have the choice of doing misc's interpretations are both For who now we only use the measurements. So you only need to put you only need to put the misc values The interpretations. It's up to you if you want those So step number one who's put start date and date put misc and in the upper right hand corner There is an icon that has an arrow. That is the export icon. Let me make that a little bit bigger In fact, it also has a cd there The idea there is that this is to export the data and optionally to save it on a cd We don't need to save it on a cd. We just put it on a memory stick But this is the correct button. So it says up here upper right hand corner export And if you float if you just leave the mouse there the word export will come up And then once you select the start date and date you do have the abilities to select the organisms But do not do that If you select some organisms like eco like club chelicinomonas It will export those three organisms it will only export the ones that you select If you select no organisms It will export the entire thing and that's usually what you want as long as you're exporting data You may as well export everything. So don't do anything with the organism box. So we will export everything And then and then at the top you click on that export button When you click on the export button You get the next screen Found 11 isolates continue with the export. So it has not exported the data yet. It has found the data to export Um, and you can see if it matches your expert expectations If it finds zero isolates something's wrong if it finds 20 isolates and you're expecting 200 Which is what happened at ephi Then you want to think about why is this not working correctly? So continue with export. Yes, I do. So I click on yes And then of course you have to give it a name. You can call it january 2020 Call it, you know, whatever you want Um, you can put it onto a memory stick and that's what I recommend usually it's convenient Stick in a usb memory stick and then the data will go directly to the memory stick Uh, you have two other options. You could save it onto the hard drive You can put onto the desktop you can make a folder for the by default Vitek wants to put them into this folder called lab files You can put them there. You can put them on the desktop. You can put them anywhere you want Uh, or you can put them onto a cd, you know, there are viteks where the usb has been disabled Uh, why would they disable the usb? Because the company does not want viruses They don't want people putting anything they want the vitek and games and so on a very small number of viteks The usb option has been disabled for purposes of vitek protection So if for some reason you cannot use the usb Then uh, then you can just save it to a cd and these instructions also provide instructions on how to do that But most people do not need to say save the data to a to a cd Okay, so you can save the data to the hard drive as I mentioned you can save the data to the to the network to the to the um hard drive to the to the desktop That's fine. It's there on the desktop But usually you don't have whoonet on the vitek machine Vitek is a windows computer technically. Yes, you could install whoonet onto the vitek machine But I don't recommend that or more specifically the company doesn't recommend it As I said the company does not want viruses and incompatible softwares They don't want to run out of space So even though you might be able to put whoonet onto the vitek machine In the united states, it's forbidden. You would void your contract Because they're trying to pretend that they don't they have to provide technical support all over the country For good reasons. They don't want to provide technical support to labs that have put viruses onto the machine That's not a good use of the company time So that's against our policy and our contract, but even in your case It's really not a good idea to be installing new softwares onto these machines Therefore most people simply put the data onto a memory stick And then they click on this last option called export inactive isolates One comment about export inactive isolates vitek distinguishes between an active isolate and an inactive isolate um It's exporting only the inactive ones. So make sure like I was in a laboratory in belarus At the national center and we exported the active data and it only exported like 10 isolates And I asked them a few questions and they said, oh, yeah, we don't finalize our isolates. We just leave them pending forever um That's the only place I saw that really here's the hospital will always finalize you know vitek You have these green and the red circles green is fine finalized and um after a certain time they automatically get archived So export inactive isolates if you're not seeing the data that you're expecting it might because you have not finalized your results That was not the case that dphi. I think everything was finalized in the normal way So it's not exporting all isolates exporting the the archived inactive isolates And then at the bottom you see a progress meter And export finished 100 it does take a little while to get started. It might take 10 seconds 20 seconds for to get started Once it started it usually finishes in a matter of a few seconds like maybe five more seconds Obviously depends on the data quantity, but okay, so when you click on export it does take a little while for the export to get started And then the following instructions here tell you how to save the data to a To how to save the data on a cd, but i'm not going to cover that because at ephi. We were able to do the usb approach So are there any questions on how to export the data out of a vitek? In short start the vitek and log in Click on toolbox export inactive isolates Put a start date end date m i c Don't choose the organisms because then you'll only get those organisms and then finally click on export Give it a file name usually on the memory stick and Yes, and then you will have all of the vitek data that you've selected on your memory stick You take that memory stick from the vitek computer and you walk over to another computer where hunet and backlink are installed Are there any questions on that? Okay, maybe question John, maybe I have one question regarding exporting this data turn Uh, yeah, uh, you know, uh, vitek We'll export only text data, right? Text yes Yeah, maybe I don't know. Maybe this vitek can give us excel data excel type Nope, it cannot It cannot okay. One of the nice things about the vitek export is that it is completely easy and non configurable That makes it easy A limitation is that you can't change it. It is what it is Any vitek in the world you go to the vitek and you're going to get a file I will now show you what the file looks like. I will show you two versions This is a file that I received from ethiopia And here you see all the vitek data Okay, I see the heading at the top. I see the first column is called lab id Isolate number patient name patient id patient location And then here I see The results it's the specimen number is 50042 PUS isolate number one um Patient name id location are all missing Uh followed by the specimen date is 2014. So again, it's that thing It's the it's not really 2014, but we had to trick the system so it could use the expired panels The organism is streptococcus mitis abbreviated in a non-standard way STR for strep mitis SMT is the code followed by this number here. This number is called the bio number Or the bio type The bio number It's like an api So, uh, there are 20 the for vitek. There's 16 biochemicals And and you incubate it in the vitek overnight if none of the biochemicals change color Then this biotype is 000 000 000 If some are positive and some are negative Um, I'm sorry. They're 48. They're 48 biochemicals 48 divided by 3 is 16 So this 16 digit number is a summary of the 48 biochemicals So knowing what this biochemical number is Tells you what the species is So generally, there's really absolutely no reason for you to know this long number Uh, because it's what vitek uses to tell you the species. You just need to know the species Having said that I personally like to see this number because there are many different numbers that would be e.coli Many different numbers that can be e.club siella. So for my outbreak investigations I do like to see the bio number because it provides greater discrimination Instead of just calling it e.coli which e.coli is it? Low discrimination means that this is its best guess Strip mitis is the vitek's best guess And the vitek is at trouble with these Strip viridins things. So what you want to see is excellent identification This is a staff aureus Excellent identification 98 percent certainty. That's called probability 98 89 We think this is an enterococcus facalis, which is a pretty good But it's looking for at least 90 percent. So vitek is saying my best guess is enterococcus facalis. I'm pretty sure I'm 89 percent sure So i'm telling you some details about the vitek that are not extremely valuable for data analysis But personally I do like them Because it does help us, uh, you know, I find an outbreak investigation To look at the resistance phenotype but also to look at the biochemical phenotype, which is what this number is telling me Here you see 000 it says, you know, non-reactive means that nothing nothing grew nothing nothing happened Okay, I'm looking at this file right now in in a text file But I can also open this in excel. So let me close Let me close that and let me go to excel I'm going to do open Browse C drive Ethiopia data It's now says all excel files. I don't want to see all excel files I want to see all files, which is the first option at the top of the screen And here's my vitek data I'm now importing these vitek data into excel Is this a delimited file or fixed with it's delimited the limited means separated And here you see there is a separator John commas telling comma e coli comma uran Everything is separated by a comma. So that is what we refer to by delimited the data elements are separated I say next And then my mouse is disappeared. I don't know why so but it's not a problem It's just I will not I usually use my mouse to show you where I am on the screen But my mouse is not working right now. So instead I am using my finger Okay, so at the top you can see excel wants to know is this a tab delimited file John tab stelling tab e coli tab uran. No, it's not it's using the commas So I'm putting comma here I can get rid of tab. I don't have to there aren't any tabs here So it doesn't really matter whether or not I remove the checkbox for tab I will say next And it's asking are these date fields or text fields. I'm just going to say general and let excel figure it out It's helped sometimes corrupt data, especially dates, you know, it thinks it's a date or it's not a date or it it confuses month day day month or You know, sometimes you have these m i c values like in trimetha from sulphur Um, you'll have it. You'll have um a value like um, you know, 119 One microgram of trimetha prim 19 micrograms Of sulphur mythox is all and excel will get confused excel thinks that 119 is january 19th So, um, if I care about the import, I'll be very specific. That's text. That's a date That's general. I'm just going to put general because I'm not going to use excel to save the data I'm only opening the data to show you the data in excel. So because I'm only using data to view the data I'm just going to say here general because I don't care if excel accidentally corrupts the data Because I'm not going to save the data So I'm just leaving this on general. I click on finish And here are my data in excel. Let me just make this a little bit wider so it's easier to see So here you can see you saw how In notepad the data are kind of easy to understand, but it doesn't really line up very nicely Whereas when I have this in excel it lines up in the nice normal way of rows and columns So for example, if I turn on my filter I can see my dates here go from 2014 and then jumps up to 2018 2019 Hopefully we finished with the expired panels I can see my Organism name my organism code my bio number and you can see excel is a bit confused It thinks that the bio number Is a number and it isn't it's really text so that e to the plus 13 Is a little bit of a corruption. It thinks this is a I think this number is 41 trillion So this one this column would have been better to treat as text Uh probability uh the organism and then here on the right normally I would see the antibiotic results And as we saw in the email at ephi then most they use the vitech for identification Not for the antibiotic results. So that's why I'm seeing my identifications here, but I am not seeing the antibiotic results So this is the data file from Ethiopia I am happy to say there are no patient details here We'll talk about this later, but please don't send me anything confidential in the United States. We have a law called HIPAA You're not supposed to be accepting things without a data sharing agreement, especially with things like names states of birth Hoonat has had for a very long time a feature for encryption About two weeks ago one week ago. I forgot when we released it We made some new features in Hoonat for encryption and I can show you that I'm going to take a little detour and show that to you now I don't know if you have this version of Hoonat yet and it's not the subject of this call But if I go to data entry, there used to be a feature called encrypt We have now merged it. So it's now we use that one feature called encrypt Another feature called combined export or encrypt. We just put it all together So here there's an option called encrypt That's always been there encrypting. He's always been there, but now you can configure it There's different people have different levels of Desire, you know, maybe I do want this and I don't want that. Let's talk about this later But in the version the the recent version of Hoonat has an encryption feature that you cannot change This newest version of Hoonat has an encryption feature that's smarter that gives you more control For example specimen date. Should I leave the date? Should I change the date? Should I shift the date? My patient name. Yes, let's get rid of the patient name But there are other things that are a little bit in a gray in a gray zone No, should I put the month of birth or the year of birth or should I delete the birth? So this new encryption feature in Hoonat gives you more control Over what should happen with each of these confidential fields? So that's a little bit of a detour about encryption Let me go back to my excel So I was glad to see that there's no patient details here But in the future just don't send me anything Unless if we've discussed it first in part if you send me things a lot of times I really don't have time Somebody send me something. I want to analyze it But I also don't want to analyze things that I that we haven't agreed to So, uh, good. Okay. So this is what a vitech file looks like without antibiotic results Jonah, I have a question please Go ahead How can we uh change the active file? Into inactive files Because we export as you show us inactive files So what does that mean active me? Is that two days or one days? So how can we get that recent data? Uh to export By inactive form. Thank you the the I'm not an expert at that because the best person to answer that question Is the vitech vendor and this is part of their job. So, you know, I could see export as somebody wrote in the email that You know, uh, sometimes the vitech people usually the vitech the biomary or representatives are extremely helpful Because they see this as a competitive advantage That they're offering a service that other companies cannot And a lot of times they want to have a good personal and professional relationship So most cases the representatives are extremely helpful But sometimes they are not helpful. They're not available or sometimes they simply do not know the answer to that For this question, it's part of their normal job. How does an active isolate become an inactive isolate? Uh, I can give you an approximate answer. I'm not exactly sure on the screen. It comes up in red the inactive I'm sorry the The right the incomplete ones come up in red And you actually I I'm guessing you have to right click on it finalize Or click on it in somewhere at the bottom of the screen. It will say finalize the reason in Belarus Uh, that they were not finalizing is they said we we we don't have all the information That are that's needed to finalize it and we just got out of the practice of it Um, and they said we don't do clinical reporting. We're just providing reference services And they had a relatively small volume of data at the national level So the Vitek in the hospitals were fine So how do you how do you finalize an inactive isolate? I'm not certain You right click on it or search for the finalize button There is also something like automatically after 14 days or 30 days to move things to an active So I have given you an approximate answer But the truth is I really don't know exactly When I'm there at the machine, I kind of vaguely remember because everything's on the screen I don't usually go to those screens. I go to the export screen. I don't go to the data specimen processing screen So it's it's easy to do but if it's not obvious on the screen Just ask your vendor because this is part of their job. How do you how do you archive? Because I don't even think they get archives Uh, if they are active and of course archiving is a core element of any machine to back up the data Is there somebody on the phone now who knows the answer to this question? I don't hear anyone. So I think I guess the answer is to that. No Okay, and it'll be clear on the screen. They'll be in red. So if you see a lot of things in red, then you're then you're not be there Then they are not inactive They're not archived Okay, uh, the vi-tech is another software as a few other softwares. There's one called myla. There's one called observer This is especially for epidemiology or for in interfaces like my hospital We have the vi-tech machine with the vi-tech software. We have the hospital information system in between We have the observer or myla software that does the interface So the advantage of the observer is the observer does export the inact Observer does export the active isolate. So if you have the observer, but you don't I know that because you don't have the interface Um for people with the observer or myla I'm not sure but for observer it does both the active and the inactive isolates So this this would be a proper answer for somebody else But for you, you don't have the observer. So it's not relevant myla. I'm not sure whether the inact whether the active isolates are there or not So I've turned to what a vi-tech file looks like and as you can see this is the kind of data that who not wants But not in a way that who not understands For example in who not we don't call it a collection date. We call it specimen date We don't call it specimen type. We call it specimen We don't call it patient ID. We call it identification number. Do you see everything here is what who not would like But the names of the columns aren't the same In addition The organisms, you know, they call it smt. That's not the who not code. That's their code In fact, some of them might coincident to the same like e coli is e co that one who not and vi-tech use the same code you know, but these other ones, you know, I don't you know, I You know these other codes like who not enter a caucus vicalis and who not is efa and for them It's sfl. So these organism codes mean nothing to who not they mean a lot to vi-tech but not to who not And also these organism names don't mean anything to who not Or to backline, but they help us get us there. So we are going to even though they have the organism names They are not in the who not structure. So even though we have basically who net kind of information here Backlink will not understand it who net will not understand it because the names of the columns are different And the names of the organisms and antibiotics are different So that's the purpose of backlink is to take this vi-tech file And to make a who net file out of it So we're going to change the names of the columns change the names of the codes So that's what we that's the whole purpose of backlink in short We have microbiology data here that who net would like to understand what we need to help it out This is what a vi-tech file looks like that has no antibiotics in it I'm not going to close this file file close safe changes. No I'm now going to open file open So uh by email somebody asked me if I can show some real vi-tech data with antibiotic results And fortunately when we distribute who net around the world, we give you a sample file We give you one sample file for excel one sample file for vi-tech I'm going to go look for it now. I'm in excel open and click on browse I go to my who net data folder And I see all files. So normally I have to change this from excel, but I've already done that. So see all files Here is a file. We will talk about later for importing excel demo excel data But that's not the subject right now There's a file that all of you already have If you go to your who net data folder, you will see a file called vi-tech to demo data And it's a small data file with real data And it's a small data file with real data I'm going to open this file in notepad, but now open it in excel. It will just be more interesting and easier to discuss So I'm opening this up in excel delimited yes tab no comma yes next I'm going to go to that column called bio number bio number there it is And you see how it says general. I don't want to treat this one generally I want because then excel is going to think it's a number because it certainly looks like a number But it's not intended to be read as a number. It's like an api number. It's it's it's really a text string So I'm going to say this is text And I'm going to say finish And now when I go to the bio number column I'm trying to do this with my file. I can do this with a Great. So now you can see this is handling it like a like a real like a like a like a text It's not changing it to 10 to the 16th power or anything You can see for the staff of the caucus It has this many biochemicals times three for a gram negative. It has more biochemicals, which is why the bio number is longer And again, I'm we're not going to use it. I personally like it But it's not nor it's not common that people take advantage of this additional typing information Okay, here's a new example where it thinks it's a number Let me let me import it again file open by tech demo import delimited comma And I'm going to say the first column the lab id is text And I'm going to say that the bio number is text And then it does not change the formatting It doesn't treat it like a number. It just treats it like the the a series of digits So now that you've already seen this and you can see Every by tech too in the world the data look exactly the same. That's one thing that makes it so easy They're all the exactly the same There are differences in the dates is it month a year year month day that depends on the machine But the organisms are the same the antibiotics are the same Uh, the specimens are different the by tech company gives you a list of organisms and antibiotics They don't give you a list of specimens. That's locally defined The column headings are identical And let me just make the column headings a bit wider. So they're easy to read Okay, so you've already seen all of this on the left so far the new thing here are the m i c columns I see cipro. I see clinda mycin. I'm going to go to the trimetha primsulfa Uh, okay, and here you see it's a little bit different trimetha primsulfa is a mixture of two drugs Um, uh trimetha prim and sulfa. So when you see here, it's the 20 What it is is it's one microgram of trimetha prim And 19 micrograms of sulfa methoxazole So at the top you see this is two drugs trimetha prim and sulfa So the by tech just adds those two numbers together to get a 20 That's what a by tech does by tech Micro scan instead, uh says 119. So what by tech calls 20? A micro scan calls 119. It just lists the two values separately and what who not does Is it just puts one, you know, because it just puts the value of the trimetha prim Because it's just easier to deal with one two four eight dealing with 119 Is difficult to put onto a graph But one two four eight is easy And the 20 is just strange most people, you know, so these three numbers So sxt is just a strange antibiotic because it's two drugs So if you see a 20 a 119 or a one, they basically mean the same thing. They're just formatted differently That's a special example. Everything else is here is pretty normal Greater than equal to four for greater than equal to point eight The oxycylence green test is simply positive or negative um One of the things that people think is that people think that the by tech is an m i c machine That's sort of true But as you can see the by tech verily rarely says that the m i c is equal to something What the by tech usually says is it's less than or greater than Meaning it's not an m i c. It means it's greater than this or it's less than this So here you see the the m i c. I don't know what it is But I do know that the m i c is greater than or equal to 16 Here the m i c. I don't know what the m i c is, but I do know it's less than or equal to one So the m i so the by tech if you look at this, I would say about 90 of the time By tech doesn't tell you exactly what the m i c is by tech tells you it's greater than this or less than this So here the by tech is equal to four equal to two equal to two, but here it's just simply greater than or equal to 16 Another small formatting issue here. It says greater than equal to eight. That's what by tech says Microscan, well, let me just do this in a slightly different way. Let me put this on a new thing here So by tech so so let's so let's just say that we are testing Dilutions let's say we're testing a test tube that has one microgram per milliliter uh two four Okay So let's see that we have test tubes and the first test tube is one microgram per milliliter second two test tube two third micro third test tube four and if the bacteria has no growth No growth no growth Then what we say Is that the m i c is less than or equal to point less than or equal to one Okay, so this is just I'm just explaining the basic principles of the m i c test If you are testing one and two and four micrograms per milliliter and the bacteria is unable to grow That means the m i c Might be one because one inhibited growth, but it might be less than one So m i c is less than or equal to one That's isolate number one Isolate number two, maybe there's no growth growth growth And then the m i c is equal to two because two is able to inhibit growth and isolate number three no growth of Yeah, that's right. That's right. Let's see the bacteria grows growth bacteria grows bacteria grows Meaning we were unable to inhibit the organism. So this is the m i c is greater than four So the four did not inhibit growth. So the m i c is something greater than four So the so if you have a micro scan We call this greater than four if you have who now we call this m i c greater than four Do you have a phoenix? m i c greater than four E-tests m i c greater than four Every normal person in the world m i c is greater than four Except for the vi-tech Vi-tech says it's greater than equal to eight Which kind of sort of means the same thing So, um, I really I probably shouldn't have explained all this to you, but you know, I'd like to tell people stuff If this is confusing to you, I'm happy to re-explain. It's also not so important It's a little bit important because when you see m i c greater than equal to eight Back things will automatically change that to greater than four because it means the same thing We just one two four eight sixteen So if the m i c is If the bacteria grows in four that means the m i c is not four the m i c is greater than four But the vi-tech says, you know, it's not four, but it's greater than or equal to eight So all of these things here that you see mean exactly the same thing So I guess the reason that I am explaining this is that some people tell me john Backlink has changed the m i c value because the vi-tech calls are greater than equal to eight Vi-tech calls are greater than equal to eight, but who net doesn't back think will automatically change that to greater than four So they mean the same thing. So don't worry about it if back link is changing your m i c It's not exactly changing it. It's just reformatting it So the reason I explain this is just to explain why the we're just reformatting it just to promote Promote standardization across all who net users So m i c of greater than eight Means exactly the same as an m i c of greater than or equal to I don't know if I said that right an m i c of greater than four Means exactly the same thing is greater than equal to eight because we don't test the The dilutions in the middle we only test one two four eight sixteen. So if it's not four, it's eight or higher So it's a formatting difference It's not an m i c change. It's a formatting change So these are what vi-tech data that look like that have antibiotic results Um, all right, they're also small issues here. You see less than at the point one two Some other machines call a point one two five You know, it's just round off errors. Some of these systems even call a point one three They mean the same thing. It's just it's rounding off differently But with the vi-tech it will always be point one two I think with the micro scan is point one two five. I'm not quite sure So so far we have talked a lot. We have not talked about backlink yet. We've talked about the original data file We covered how to export the data from the machine I'm showing you what the data look like in excel You don't have to do this. I'm showing you what the data look like in excel But there's no requirement that you do this you can go directly from vi-tech to backlink So why am I showing you the data in excel? Showing you just to you know, just to give you a sense of what backlink is doing Showing you what the vi-tech data look like when a vi-tech makes it And we'll show you later what it looks like after backlink is finished with it That's one reason why I'm showing you what the data look like in excel Another reason is for is for data checking sometimes people tell me john i'm analyzing my data But there's no imipenem results And they ask me john why why am I not seeing my imipenem statistics? And there are three easy they're four easy answers But I I can't tell them So they say john I can't say the imipenem results. Why can't they see the imipenem results one if they didn't test it You know maybe the national data manager is saying I don't see any imipenem results from laboratory number six Why can't I see the imipenem results? Reason possible number one. Maybe they didn't test it. Just ask the lab. Did you test it? reason number two They tested it, but it's not in the export With vi-tech that would never happen vi-tech always exports everything Um, so the reason number one they didn't test it reason number two the system didn't export it Reason number three back thing didn't import it. Maybe they didn't find it Maybe back thing did not recognize imipenem or reason number four. Maybe who that's not looking for it Um, so whenever people tell me something is missing. Where are my january data? Where are my blood data? You know, for example, if the date formatting is wrong, you know, if who net thinks you have month day year data But you don't have your month. Maybe you don't have month a year. Maybe you have day month year Maybe accidentally the month of december will disappear People say john what happened to my december data? So the first thing I will do well is I'll ask him Well, do you have any data for december and they'll say well, let me check and I'll say yes We do but then what I will do is I'll go to excel and I will open up the raw data file Because the raw data file will tell me are the data there Are the is the column there are the results there? Or the dates in the right format So whenever you're something's missing the first thing I want to do is I want to look at this in excel Because if there's a problem with back thing a problem with who net we want to fix those But I don't want to focus on back think and who net if the data the original data are incorrect So that's why one of the reasons is showing you I want you to be comfortable importing polytech data Or vitec data or phoenix data into excel because this is going to answer a lot of your questions Why is something missing look at the original data if they're missing from the original data Either they didn't do it or they didn't type it in or they didn't export it So it helps you with debugging trying to understand why certain data are missing or the dates are corrupt I'm now finished with my discussion of the vitec files and the vitec export any questions Otherwise, I will move on to backlink It is the same to extract data from polytech the one you told us all this process No Because you know I showed you the I'm going to go back to word I'm going to back to the back think word document So I showed you when you open the backlink software This is what the back. This is what the vitec software looks like. There's a toolbox you click an export You click a net active and active for polytech the screens are different the steps are different um, I um I never made this into a manual with your assistance. It would be great if we could make this into a manual I don't remember where I put this. Let me try this um Let's see. Let me go to Um, and then we go to examples And machines And polytech do I have any screen graph 2019 export data tags? Let me open this up Okay, so, uh Some of you are familiar with polytech and this is what the screen looks like Record selection. So you see the concept is the same You see at the upper right hand corner start date end date Do you want to export list you want to export the output file as excel? Do you want to sort by this? um, and you see at the bottom of the screen it says uh edit format You user export and export data. So you can see the concepts are the same as the vitec But the screens are different Here it says edit format vitec doesn't let you do that. So one advantage of polytech Well, one disadvantage is that it's it's more confusing and more work Uh, but also it's more configurable So the bite one disadvantage of the vitec export is vitec data Unfortunately, the vitec export does not include age and not does not include sex So even if you type those data into the vitec machine The vitec export does not include it which is very unfortunate They fixed that with so observer always had it. Myla has it So hopefully this will always be their standard in the future But if you are entering age and gender into your vitec machine In the age and gender column Unfortunately, the vitec exporter showed you will not export it and there's nothing you can do about it What some people do is they is they put the age and the gender into some other column that does get exported They trick the vitec system. They'll put like the they'll put the They'll put like the specimen type plus the gender. They'll put it somewhere. Um So one one disadvantage of the polytech export is that it's more steps. It has to be configured But that's also an advantage because you do have control over what is and isn't exported So here you put a start date and an end date You oh, I guess we did a better job. I guess I did a better job than I thought So I won't go into this or maybe maybe, you know, this might actually just be for the company. I don't know It's usually the export and then here is what this is what polytech exported data look like Oh, yeah, I think I just got this from the company because these are not Ethiopian names Okay, so in answer to your question No, the export from every system is different you go to the software and use the interfaces on those softwares So the principle is the same go to the screen put a start date end date Maybe configure it on the system the two systems. I've shown you this is on what we call the front end The user can do it Other systems there is no front end for data export So for those people you go to the back end and you ask the it people to export the data So I'm going to close this polytech instruction manual Uh, I'm going to go to polytech export microbiology data Let me open that up So this is the uh, I don't Right. These are also not real data. This is just practice. So you can see the polytech. Let me make this bigger The the polytech sample ID patient ID patient named species glucose thyroid stimulating hormone potassium carbon dioxide organism s-needobacter Um, beta hemolysis. So on my first trip to ephi we figured out very quickly how to export the data But we cannot figure out how to export the antibiotic results So that took the second visit. I had to come back to boston discuss it with the company They gave me the software. I do have a copy of polytech on my machine The the my license is expired. So eventually I will show you how to do this with polytech But I need the company to um, you know to react to me reactivate my thing here So an editor question Again, every machine is different. How do you export data from the system? I know how do you export the data from bytech? I can tell you Polytech I can tell you except I always forget the details. How do you export data from phoenix? I can tell you How do you export data from? Laboratory system from hospital number four. I have no idea. I don't know that system. I don't know those people I don't know the it people So instead you need to work with those it people to learn how to export the data and for that purpose I'm going back to who net documents We have backlink number three Backlink and lab information systems where we give guidance to the it people on how to export the data I'll just leave it at that and we can discuss that on a future call if needed We don't need to do that for bytech. We don't need to do that for polytech Because we can just focus on those systems specifically But if you have excel or if you have a lab information system, we can have that discussion as the need arises Uh, also just a general comment whenever I teach who net and back think I want to be very careful when I teach backlink For a few reasons one is most people don't need it If I go to a hospital, I teach pharmacy microbiology infection control infection disease it lab staff I teach everybody who net because all of these people can benefit from analysis I usually only teach one or two people backlink Maybe the it person or the person in the laboratory responsible for data management So one reason I don't teach backlink to everybody is most people don't need it The other reason I don't teach backlink to everybody is a lot of people get confused by it Which is reasonable if you've worked with a lot of excel data or access data or data in general Backlink is straightforward. I don't want to say backlink is difficult But the concepts are new to a lot of people So for a lot of people they do get confused by backlink because it's the first time they've done something like this so Same way for you Another reason I don't teach backlink to large groups is that even if everybody needs backlink This person needs backlink for vitech. This needs backlink for polytech. This person needs backlink for excel So instead of teaching everybody everything I just teach them this the points that are relevant for them Um, so yes, you can see your polytech can export anything I figured out quickly or maybe it was there predefined. I don't remember We figured out quickly how to export the organism results But it took a long time to figure out how to export the antibiotic results And I needed the assistance from the company to do that And then I during my last visit last february a year ago I did did a dphi. So it is there. So the configuration of polytech I did already So I said you can see how I did it is then you could optimize it. You could add more things You could make it your own But the configuration step first draft has already been done Other questions before we move on to backlink Yeah, I have actually questions Regarding the polytech Actually, I have I have tried to export the polytech data using excel format Yes, but the the data what I see from excel was, you know, one patient will have multiple rows of excel That means from the excel sheet One patient will take three or more than three rows Yes And by different rows, do they have different antibiotics? Yeah, different. Yeah, yeah, exactly When I went to the polytech there were like six different export options So one of the export options is the one with the antibiotic results So what you're so this is I'm going to show you a screen. I'm going to jump ahead a little bit Quickly and then we'll come back to it in the normal speed So if I go to backlink a new format in ball structure and antibiotics So here you can see I'm on the antibiotic screen antibiotic configuration screen or backlink and you see to you see a question here in the middle of the screen The antibiotics of one isolate Require one row how many rows of data the answers are one row or more than one row So basically both of these are about both of these are reasonable answers But it depends on the file when you put the data into excel And all of the examples I showed you so far One row equals one isolate with many antibiotics So for excel the answer to this question is one row all the antibiotics are on one row But you mentioned example where it's not one row is one isolate The example you decided is one row equals one antibiotic So in that case you have more than one row for each isolate So the who not way all the antibiotics go horizontally in one row But when you export data from different lab information systems For by-tech, it's the same thing for by-tech one row is one isolate but for polytech And for phoenix and for many others it's just easier for them that one row equals one antibiotic So you have pointed out. Yes, the polytech export is different It has the same kind of information that by-tech has the same kind of information that who net has but it's organized differently And one of the main differences in organization. It is not one row for one isolate It is one row for one antibiotic Does that answer your question? Yeah, so can we Change this data to who net Yes, yes, you can because and that's why this question is so important So back they can handle it either way back. They can handle one row one isolate or back They can handle one row one antibiotic and that's why this question appears here So that you can take data from diverse completely different systems And put it into the who net structure The who net structure is one row one isolate So in your case, it's going to flip it if you have 10 rows with 10 different antibiotics in polytech In who net that is going to be one row One row with 10 antibiotics going horizontally Does that answer your question? Sorry, yeah, yeah, you answered exactly but my fear is You know sometimes We will have ID issues Like patient ID issues So in that case, I don't know I don't know who net can consider consecutive rows of Uh No, the answer is yes the answer the answer is who net back because no trouble with it. That's where we ask the question So it all so when you have one row for each antibiotic, let me see if I can find uh, let me see if I can find a um Polytech example No, those are not data files And these are all old variables export See this one doesn't have antibiotic results. Let me go back. Let me go to a different Um Do have an example somewhere Yeah, I often delete real data. So it's a good chance. I don't have the data anymore. No Um, I'll show you a different. I'll show you a different example from a different system Now which would be a good example this? Yeah, cernar. Let me see if I can find some cernar data Cernar millennium No, there's an these are not data No phi Okay. Well, it's not a real data. Let me this is a part. This is a good example, but there's only one row So what you're describing is this situation? Yeah, yeah of a genoise and ctx and we pen them Yeah, I'm just making up some data here one four 16 of 16 greater than equal to greater than 16 and 0.5 Okay, so what you're describing This is r and that's r. Okay, so what you're just so the first every example I've shown you except for this one Every example has been one row with all of the antibiotics But this one is different. There's one row All right previously one row is one isolate Now we have one row Equals one antibiotic Yeah So I'm going to reformat this Let me I'm just going to simplify this a bit and and Let me put this Let me read the interpretation. Okay. So here you can see vertically six antibiotics Here is the exactly the same data But now it's in one row these two data are exactly the same. They've simply been organized differently So most of the examples I showed you so far are like this one row is one isolate But serner the example I have in front of you as well as polytech that you've seen There's one row for each antibiotic Back link is no trouble with either back link is perfectly happy with either For the excel example, we say one row one isolate But for the polytech and serner it's one row is one antibiotic In other words, there's more than one row because they're multiple antibiotics Similar question are the antibiotics in a fixed sequence So in this excel in this kind of example the antibiotics are in a fixed sequence It's ampicillin and then cipro and then germicin In this vertical there's no intrinsic sequence. I could put I could have put the cipro first the order doesn't matter here So that's where we have these two questions when you have excel data. The usual answers are one row in a fixed sequence But for polytech and for serner, it's more than one row and a variable sequence So does that and back think has no trouble with either back think will Understand it and spit it out in the correct two net structure Does that make sense? Yeah, exactly Right, so I jumped ahead. I'm going to repeat what I just said, but in the normal sequence of things Okay, so I'm going to close my excel and close this and then close that and close the other I'm now ready to show back like before I show back like any more questions Yes, I have one question actually our challenge Is how data is Communicator to physicians from the lab through either from money to politic as this kind of communication. So we have a very difficult communication system actually we have a challenge to communicate physicians immediately from unit Through polytech because most of our laboratories use Polytech so what do you advise to facilitate communication between the lab and the physician? Okay, um so one first of all and One of the things that polytech is now working with you on is a web version of polytech Where clinicians can log in and get their results So I strongly recommend the use of polytech because that's what it's made for partially Is for clinical reporting. So in two aspects There's the new polytech web And one of the goals of polytech web is to help this kind of national communications and reporting The initial focus of that project is cobit, but the same platform can be used for anything So that's the new polytech web teacher um, there's also at at um at tiger lion. I always get the name wrong the black lion hospital um the the black lion hospital um uh They have the polytech Interfaced with another software. What's the name? I care smart cave smart care The phi sorry, sorry. So polytech is interfaced with smart care. So smart care Is using smart care is making the results available to clinicians And they can use that for all of the laboratories except microbiology Why because they're not putting the data into microbiology We designed whoonette as a data analysis system an epidemiology system a very simple system preclinical reporting using pieces of paper And it's not adequate compared to smart care compared to polytech for web Eventually, we'll have a web version of whoonette, you know, it's on the back burner. We're getting back towards it But an editor question I would If you have your data in if you have your microbiology data already in polytech Then discuss it with jeff fisher and craig craig, you know at the polytech company and ask them How can you do microbiology culture result reporting to clinicians using polytech web? And then he can give you and then they can set it up and then they can teach you how to do that Or at the black lion hospital Try to get them to enter the results into polytech because even if it's more work for the lab And polytech is not polytech has problems from microbiology Of course, I wish they would make it a better system. It's an old system But if they can use it and they can optimize it because they're not using it in the best way for even its limitations There's certain things they're doing that are not optimized. It's not the right antibiotics. They're doing too many steps So if they could better utilize the polytech system If they start utilizing it, even if it's more work for them It's going to be of hugely great value To all the doctors in the hospital who can get the results easily So even if it's I don't want to say the polytech is going to make the lab work easier But it's of so much great value to the clinicians It also will make it easier for the lab Because they won't have to answer the phone call all day people won't be coming down to the lab Look at the notebooks. So so even if it's more work entering data into polytech than writing it onto paper It's still going to be a value to get the data into the system It's not specifically for honet, but because of clinical reporting medical archives If the doctor wants to know the patient's blood culture results from last week then can walk down to the laboratory If they want to know the blood culture results from a year ago, you can't look at the notebooks You want a computer system a lot of times you don't know if the patient had results in the past So i've made this point many times honet is not Was not intended to report online to a hundred doctors smart care was And polytech web. I think also is So uh, does that answer because I uh, honet we're a team of two three people We cannot make a comprehensive lab clinical information system for everybody in the world Customized their needs and if something breaks down we cannot be there 24 7 Uh, that's the purpose of these companies. You pay the company to do that for you the smart care company the polytech company The hospital it staff Other questions about that I have a question. Did the polytech company install the polytech web for you yet for covid reporting? Uh, in a black lens. They don't uh so far start testing covid test Usually it is original laboratories that started covid testing So black liana still the lab didn't start uh, covid testing. That's fine. That wasn't exactly my question Has the company installed polytech web for you eddy phi Uh, maybe diet knows if diet can answer this question. I don't know who installed it diet Actually What not I'm sorry the sound quality is not great. I didn't really capture that Uh, also I do see the 11 Oh, no, that's I try questions. That's just people never mind. Are there two questions? That's right. Can you repeat that? Uh, good question. Has polytech web been installed? I don't think it is the installed. Maybe we'll give you some but I don't think it is installed Right because because if polytech web is installed the first focus is covid But you know, they can set it up at some point For everything you do, I would imagine for hepatitis and syphilis and lead and all the tests that ephi does I think that one objective of polytech web is to allow your authorized Collaborators and clinicians to log into polytech web to see the results So the polytech web should be very valuable to you at ephi to get your results out to anybody That you get permission to So, uh, so So for ephi, I would polytech web and for time for Black lion, I would focus on just getting the microbiology data into polytech Because if the data are not in polytech, then it doesn't really matter about its interface capabilities because this market is already there They're just not utilizing it for microbiology Okay, we'll do that Okay, if no more questions, I will continue with backlink. Great. Let me close this Everything else. Okay. So here I have backlink and so backlink is a language translator. You know, all of you Uh, I imagine or familiar. I'm just going to go to google translate um, and I'm going to say Hello My name is john And let me other languages Amaric and then here you see I don't know how the good the translation is especially with the word john So you can see how google translate is very valuable for translating languages Um, it's doing two things. It's converting the grammar The english grammar to amaric grammar and it's converting the vocabulary. It's changing the english words to amaric words Uh, backlink does exactly the same thing. You can think of backlink as a translator So we're gonna we need to tell backlink. We can't just tell backlink convert my data You need to tell backlink. Well, what kind of data is it? Is it polytech or biotech or excel? So we need to configure backlink. So step number one of backlink is configuration. How do we import the What language do you want backlink to read? I have an answer for the IT personnel They installed four computers for the click for kovic The IT page So so the polytech web is installed for four computers. Is that what you said? No, just a software for reporting the kovic results at ephi compound only. They have a A beginning a kind of starting initiative To expand to the other lab The IT personnel from the polytech department replay this Thank you Great. Thank you. Thank you. Yes. So please continue to discussion with polytech Of course the current focus is kovic But this is a wonderful opportunity to get things set up and the more you understand what they've done with kovic The better you will be prepared to extend this to all of the laboratory areas All of the priority laboratory areas Okay, um good. Um good Good. Okay. So backlink Backlink is very happy to tell to convert data for you But backlink needs to know two things What language is it in? Is it in by tech language or polytech language or excel language? And secondly, what do you want it to convert the january data the february data the march data hospital one data hospital two data So backlink is is ready just like google translate is to help us with data conversions But it just needs some information What do you want to convert and what data structure does it have? So the data structure, that's where we will put in the configuration details So we've already discussed that who not has configuration into botics locations data fields backlink has configuration and that's what we will see now We only have to do a configuration once you know once you tell backlink I have a polytech file and you have configured it For the month of january You don't have to repeat those steps for february march and april Once you configure your january import January and february march data all have the same data structure So the backlink configuration only has to be done once Whereas the conversion you can do that once a week once a month once a year whenever you have some new data that you want to convert So how do I do backlink configuration? When you start this on your computer, you're going to see an empty list that here I see agus avia. That's from columbia a lot of these are these are a lot of these are just demonstrations This is other algeria laboratory buff rain These are doha. These are all different countries and most of these are just demonstrations or projects. I'm involved with When you start this this this this list is empty So to get started you will click on new format And just like who net there are a series of questions. What is your country? My country is ethiopia Laboratory name. I will call this ephi vitec demo And laboratory code. I don't know. I'll call it evd So on this phone call, I won't do polytech. Let's reserve polytech for another call But most of the steps are the same But vitec is easier because you know vitec. We already know everything about the vitec So we've defined the country and the laboratory code just like we do, you know for who net And then we have two questions. What is the structure of your data and what are the codes and date formats? So let's start with file structure again It's like a language every language has grammar and vocabulary and a data file has a structure and codes So the first question file structure describe the structure of your data file I click on enter Because my mouse is not working And here at the top you have a lot more questions Uh and question number one. Do you what kind of data do you have? Is it a delimited text file? Is it an access file? Is it a phoenix? Bechton Dickinson epicenter file, which is what they have at icl Uh in in uttis. Is it copernico, microskin? We have a lot of machines here all of these in this middle section are machines Including by tech observer including by tech two. That's the one that I showed to you Cerner millennium we have from norway we have Croatia Um, okay, and we don't have polytech on this list If we could finalize and optimize the polytech export, I would simply put polytech onto this list Polytech is not on this list Not a problem. We're just going to call it delimited text But if polytech is on this list, it just saves a lot of steps because who net already knows a lot of the answers Okay, so I want to import my by tech data. So here you see by tech two or by tech compact. It's the same same software Good. So so in short file structure we need to tell backlink and Okay, I'm going to go back to the first one Here you see it says file structure text delimited I mean, it's just some simple file that backlink does not know anything about Look at the middle of the screen The antibiotic questions guidelines. Is that CLS or UCAS? I don't know Is it MIC or disk? Is it one antibiotic multiple antibiotics? So when I say text delimited backlink does not know Backlink does not have all the answers I'm now using my arrow key. Well, yeah using my arrow key. Let me do this way As I go down Look at the answer antibiotic answers in the middle of the screen Depending on the machine. This machine is a disk diffusion machine. This is an MIC machine a disk machine This machine does disk and MIC. This one only does MIC This one does disk MIC and detest. In fact, this isn't a machine This is sort of millennium, which is a live information system So you can see that if I call this a simple delimited text Backlink doesn't have trouble with that but it does not it needs more information I'm going to put this back to Vitek And you can see it already knows all the answers. It is one row for each isolate This is an MIC machine The antibiotics are in a fixed sequence and it's all MIC that there are no disk diffusion data Any questions so far So question number one for backlink is what is your country? What is your lab? Question number two. Is it a generic text file? Is it a Vitek file? Is it a polytech file? So I say it's a Vitek file and back thing says thank you. I have almost all the information I need to know I'm going to click on antibiotics Normally there are a lot of questions on the screen But I'm hiding those questions because backlink already knows the answer I'm not going to ask you a question if backlink already knows the answer to the question But I do have the ability to select between CLSI and UCAST There are it's a number of French countries still UCASFM and most of these others have already disappeared Okay, so CLSI and so in Ethiopia you use CLSI if I remember correctly And if not just choose UCAST you just choose the one that you're doing Okay, um good Sounds like okay, so Um And there are more questions down here But backlink already knows the answers and I do not have to answer them So I'm going to click on okay, and I'm going to click on save And I'm going to call this evd exit exit I did that quickly because I'm going to repeat this from scratch So here you see See drive Let's see Let's see I just want to clean up my folders here because I've got a lot of stuff that you don't need to I don't want to be confusing. I'm going to take all these configuration files You see they all ended in the letter cfg all of my configurations And um Well, just a lab convention I put them here. Okay, that's fine I just cleaned up my folder. Okay, let me let me go here I'm So I'm going to everything I just did for the last 10 minutes of speaking I'm going to repeat just to highlight how super simple it is to do this for vitek So I'm just repeating everything I just did but without really talking very much new format Ethiopia ephi vitek demo evd file structure file structure vitek 2 okay save I'll give this a name. I can call this ephi vitek demo Or I can call this evd call whatever you want save And I exit So I'm just highlighting even though I talked a lot. You saw how super easy and quick it is I'm going to do it one more time lead format So because backlink understands vitek extremely well It's asking the minimum minimum minimum number of questions So restarting from scratch new lab Ethiopia ephi vitek demo evd file structure I call this a vitek 2 file. I click okay. I click on save I give it a name. I don't care what name you give. I'll call this ephi vitek demo I'll talk to you And let me call this save And you see at the top of the screen everything that I just did has been saved into a file called ephi vitek demo I click on exit and there it is So to import data from vitek you have to do configuration first Configuring the vitek import or the phoenix import or the serner import. It's extremely simple Because backlink already knows all of the answers Let me repeat that here edit format Oops edit format My mouse is giving me trouble. Let me just restart backlink Edit format good And file structure. So you see these questions at the bottom of the screen are very important But backlink already knew the answers There's another section at the bottom that we did not look at And it says to find the relationship between your data fields and the who net data fields We didn't do this because backlink already knew the answers I will show it to you just to show you how smart backlink is Let me click on data fields and you can see the first row who net calls with identification number Vitek calls a patient id who net calls its specimen number Vitek calls it lab id Who net calls its specimen date vitek calls a collection date Who net calls it organism vitek calls it organism name You're gonna exit out of that and exit out of that and exit out of that Those are very important questions, but we didn't ask you backlink didn't ask you Because I asked the company the company told me and I told backlink So the reason the vitek configuration was so easy is because we have preprogrammed in all of the correct responses That's it for configuration any questions To import excel it's more work to import polytech. It's more work because backlink doesn't know the answer to those questions Well, this goes those on another phone call Um, but any questions about the vitek import? And if no questions, I'll just continue So that configuration I did that for one month of data for example I don't have to repeat that in February, March and April because every month The data structure is the same the codes are the same the column headings are the same So configuration only has to be done once Um, I'll just give you an example of what they did in the in the country Ireland Ireland they worked with 20 different labs and the 20 different labs Some at vitek and some at excel and some at machines and some at different lab information systems So the national data manager asked all the labs. Please send me whatever data is easiest for you And they did that And then the national data manager did the backlink configuration for everybody So if I'm working with 20 labs with 20 different systems Or with 10 different systems. It was just easier in Ireland. He said, let me do the backlink configurations for all of you So he did not teach the 20 hospitals how to Create new backlink configurations It did teach them. He did teach them how to convert data on a monthly basis So just to re-emphasize the point is If you are dealing with backlink with many different facilities You should You don't have to teach them configuration. You could just do the configuration for them and then you just share with them the configuration files Okay, great. So that's configuration Now I want to can now I want to import some data But what data do I want to import? So on the right side of the screen? I see two browse buttons The browse button at the top is for the original data file that already exists The browse button at the bottom is for the new data file that we want to create Okay, so the file the browse the button at the top this file exists So i'm going to click on browse on the right hand side of the screen. There it is browse And here you can see the vitec demo. So sure Um Yeah, I'll just do that one because that's that's my data that all of you have Because it comes as part of who net it comes standard click and open That new file exists. We looked at it in notepad. We looked at it in excel And I want to make a new file. So at the bottom of the screen we have A space for the name and location of the new data file And it says asterisk because asterisk is not a real name. I'm just going to call this test So I have the real original data called vitec 2 demo. I'm going to make a new file call test And begin begin convince and I'm going to say begin conversion So just to reemphasize for you this first file exists This second file does not exist yet, but it will exist once we finish backline And this new file that we are about to create Will have the same data the same antibiotics the same organisms the same patients, but using the who net data structure So that's the whole purpose of backlink is to take the original data and to restructure it as a who net file The name of the new net the name of the new who net file is called test that evd Let me click on begin conversion We this is this step is no longer necessary we fixed it yesterday I'm not going to talk about it because we've already fixed this Okay, okay, and I'm going to restart that. Okay Okay, so now I click on begin conversion And it is going to show me the first three bacteria So I can do a visual inspection to make sure there's no obvious mistake The left side of the screen says first name last name. That's the names of the fields The second column has the vitec value You know, this is the vitec name john smith location is icu specimen number is this specimen date is 2014 You know june 2nd blood staphemolyticus So the middle column is what backlink sees in the in the in the vitec file The column on the right is the new things that are going to go into the who net file Most of the columns it just simply copies and paste So identification number is simply copied pasted john smith is split up into john and smith icu is copied to copy to icu the specimen number is copied the bottom of the screen i'm paying closer attention Staphemolyticus is what vitec calls it So we're going to copy that over to the who net file But the who net code is shl So here you see two similar columns the who net organism code And the local vitec organism code So we just copy over the vitec code without change so we don't lose information But we recode it with the who net code So staphemolyticus becomes shl Backlink knows that because I already programmed in the full backlink the full vitec dictionary Blood it's smart enough to understand the word blood because blood is blood The vitec word is blood the who net word is blood. So the who net code is bl So you can see that backlink is doing a nice smart job of capturing the specimen The organism and then the antibiotic results at the bottom of the screen The backlink is having a little bit of trouble here with the dates The specimen date and the test date The bio number is fine. It's simply copied over the probability is copied over On this entire screen. There is only two there are only two problems both of them with the dates And the data file says it's june 2nd 2014 But who net says I don't know what that means Same thing for the testing date the dates wrong So basically i'm very happy this isolate number one. I am happy Let me go to isolate number two Isolate number two mary jones five north blood Steph hominus antibiotic results. I'm happy with this Except for the dates What i'm looking for here are mistakes. For example, if the name of the person Is sputum. There's some mistake If the name of the if the name of the specimen is staph aureus, there's a mistake So the reason who in backlink is showing you these first three is to do a visual confirmation that the data are working correctly And here i am happy everything is working perfectly Except for the two dates It's isolate number one isolate number two. This is isolate number three again. Everything is perfect except for the dates Any questions so it's almost perfect, but i've got to do something about those dates Sorry john what about sex uh and age Well, uh Excellent question. So what what you see here on the left side of the screen are the questions that who net would like to know That list you can change you can add questions. You can delete questions So the list on the left is what we would like to capture The second column here is the information it found in the vitec file So let's go back to the vitec file Let's go back to the vitec file Oh, and I guess I move uh Excel complain because backlink has this file open. So i'm just going to make a copy of this file So vitec, oh i already have a copy good. Oops. I accidentally left excel. Okay, let me go back to excel and It's limited comma open Okay, so these are the vitec data that we are importing Do you see agent section this file? No No, and the reason is very unfortunate. The reason is that the vitec export does not include it And there's nothing you can do about that. Um, it's just a weakness of the system because they made this system years ago Without thinking about people using this for epidemiology And we've complained many times the company as I mentioned observer has no trouble myla has no trouble But even if you enter age and gender into a vitec, it will not be included in this export So in answer your question, it is missing from the data file. That's why we don't see it because it was never there to begin with And that's always true for vitec, but there might be other examples You might have a different data file with male and female um and Who net is looking for a column called sex? But if the column is called gender, it's not going to find it So if so you pointed out that the gender is missing it's for one of two reasons either it's not in the file to begin with Or it is in the file. The back link is not seeing it And that's why I opened the data file in excel and in this exam in the first example I saw that it's not there to begin with and that's why it's not there And it won't be there because it's just completely missing In the second example it is here But back think might not be looking in the correct place We can fix that we can say I showed you a mapping screen before You know, I said the date of birth is date of birth. I showed you this is this we just need to match sex to gender um Okay, and we're going to repeat that later when we do a poll not on today's call But when we do an excel import or an apollitech import We will show you how to map up the data fields. I showed you the end result I showed you how smart back link was for mapping things. We didn't do it. It was all pre-mapped So an answer your question. Yes, one of the things I'm looking for are are there things you're missing? I mentioned exact I mentioned examples like if the patient's name is sputum. There's obviously a mistake If the sex and date of birth are missing Is that a mistake? I have to think about that. Well, was it in my data file if it's in the data file Then yes, it's a mistake. It's missing So you have correctly pointed out sex and date of birth is missing and the reason is that the original data file does not have this information Okay, so it's isolate one isolate two isolate three. I will now click on next And backing is running through the rest of the data file It took seven minutes because I was talking so much And it found 28 isolates So it's a small sample data file. We use for test purposes Click okay Um, and we get an important question back thing says basically I kind of understood your file to a very large degree However backing does not understand all of the codes Uh, do you want to review the new codes? Yes, but not right now. We'll talk about that afterwards In short, I am very happy with this conversion except for the dates You can even see that at the bottom of the screen invalid date 2014 invalid date and even look more carefully Invalid date it is looking for month day year But these data are not month day year. These data are year month day So basically it found the date great that part worked fine But it's trying to it's confusing the day and the month and the year That's why backing says I don't know what you want here. I'm a little bit confused I I think I'm supposed to be looking for month a year But the dates the dates are not month day year So do you want to review the new codes? No, I don't want to review them now. I'm going to review them as a separate step after No Um So now I'm going to go back and I'm going to make that correction Edit format I go to edit format So far we have only looked at this option called file structure We're now going to look at this other option called codes and dates And in the upper right hand corner of the screen You will see that backlink thinks that it is month day year and backlink is wrong So I'm going to go to the drop-down list. You see there are many options year month a day month year Just the year a lot of options The one that we have here is year hyphen month hyphen day The date of birth well, in fact, there is no date of birth in this data file So it doesn't I can leave this empty. There are there is no date of birth I'll put it in just to be consistent. But in fact, it doesn't matter because we do not have a date of birth So I have now fixed the specimen date There's one additional date I want to fix. It's not a normal date But there's a field here called modify the list of data fields I mentioned Vitek has a specimen date. Vitek also has a test date That's very specific for the Vitek. So testing date is not on the screen in front of you I'm going to click on modify the list of data fields At the bottom of the screen, you do see the bio number and the probability But testing date you can see now in the upper right hand corner is also month day year Let me change that to year month day I'm going to click on okay. Click on okay. Click on save. Click on exit. Click on begin conversion And now you can see the date is fine The specimen date is fine The testing date is fine Any questions on that? I went through the first time I inspected Everything seemed to be pretty good perfect Except it did not understand the dates So what did I do? I went back to the configuration. I changed the dates and now I'm going through a second time And I see yes that particular issue. I have now fixed Any questions? Okay seems like no questions. That's isolate number one isolate number two isolate number three Runs through the rest of the database This time it only took 49 seconds because I talked less Okay Very important at the bottom of the screen It doesn't have any complaints about the dates. So all those complaints about the dates are gone It still says back thing did not understand all of the codes in your file. That is correct Okay So now we come back to that question that I ignored earlier Back thing says great. I understood almost everything your dates are fine your data fields are fine But I don't understand all of the codes Do you want to review the new codes? Yes, I do And this is a list of everything that Vitek did not understand The first thing I want to highlight is what you don't see here. You don't see any unrecognized organisms or antibiotics And that's because back thing is smart Every Vitek in the world. Yeah, it depends on your version and your software updates But more or less every Vitek in the world has exactly the same list of organisms with the same codes The same list of antibiotics with the same codes and we have pre-programmed that into who and into backlink So backlink has trouble with your locations because every hospital has its own locations Backing is trouble with the specimen type because every country has its own language and specimens and lists So so it's normal that backlink has trouble with the local locations and specimens The backlink did understand all of the organisms and all of the antibiotics So I'm happy about that. So the first thing that you see on the screen is good That you don't have to define the organisms and antibiotics. Those have been predefined into Vitek and into backlink What we do see here is a list of specimens and locations I'm going to start with the specimens Which is more important Define codes at the bottom of the screen And you can see that I do not see here blood or urine or stool Because backlink understood those automatically It's only showing me the specimens. It did not understand So in the lower, I'm also watching the time. I do have a conference call with Egypt at WTO in In you know in 12 minutes. Okay, so I'm going to you see here. It says viewcode dictionary I'm going to click on viewcode dictionary And here you can see these codes are in my Vitek file And backlink understood them automatically. There's blood. There's urine. There's throat Backlink did not need your assistance to understand these But backlink does need assistance with sputum sample Hoonet has sputum, but Hoonet does not have the words sputum sample. So that happened 12 times I want to click on define codes And backlink is trying to help you out Sputum does that mean induced sputum? No, it does not Is it sputum for acid fast bacillus? No, it is not. Is it just normal simple old sputum? Yes, it is So backlink is trying to help you match the local codes With this that is different in every hospital in the world With the standard list of Hoonet codes so that people around the world can have different local codes for their systems But they have standard Hoonet codes So sputum is equal to sputum Catheterized urine is my second example to find codes Backlink is trying to be helpful. Is catheterized urine the same as urine non catheterized? It's a bit of a trick question No, it isn't one is with the catheter one is without the catheter So i'm going to change my search box and just search for the word urine There's a better match here urine from catheter So that's a better match I click okay I can view my code dictionary and here you can see sputum sample catheterized urine So these specimens at the top we did not need to help backlink backlink was smart enough These two at the bottom it understood without any assistance. I'm sorry. These two at the bottom We we told backlink what it is. So now it will remember for the future Okay, so now I've defined all of my specimens. Let's go ahead and define our locations So define codes It's only has to be done once it encountered the word outpatient 16 times it encountered. I see you five times So let me just start at the top outpatient This hospital calls it outpatient Hoonet also calls it outpatient as a department And as outpatient is a location type. Okay I'm gonna I'm gonna do something like five north just to highlight the differences Five north at the top five north is going to stay five north. We're not going to change it But we're going to say that five north is medicine inpatient in contrast I'm going to go to three south I'm going to see that three south Is equal to surgery inpatient And let's say, um, I'm just trying to find an outpatient. I don't see any outpatients Oh, sure cardiology. I'll call this cardiology. I'll call this medicine outpatient Okay So locations are a little bit different like your organism and specimen. I want you to match the Hoonet codes For this it's more describing the code like if your code is cardiology We're just going to call it cardiology But I would like to describe it as medicine or surgery medicine inpatient outpatient So this stuff at the top is very local and very specific These questions at the bottom are really just to kind of categorize it You know, if you're at the national level at EPHI A lot of times you really don't care about third floor fourth fourth fifth floor north south east west The hospital cares the hospital wants to know where the patient came from But the national level you're really often just interested. Is this an inpatient or an outpatient? So by defining this this will allow us and let me click on view dictionary So we're just making a list here of we're just making a list of is this inpatient is this outpatient So the columns on the left are very local specific The columns on the right are really for categorization purposes We already discussed that with Hoonet configuration The columns on the left are very specific to the laboratory The columns on the right are just standardized to permit easier analysis and easier standardization I'm going to exit out of that. I'm going to exit out of that. I'm going to continue I'm now back at the main screen I've to I fixed the dates. I defined all the specimens I defined a couple of the locations so it's getting better. That's not finished Let me do it can begin conversion one final time begin conversion Isolate number one looks perfect Isolate number two looks perfect and it even says your medicine So we're adding on that descriptive information That was not in the original data file next Three south that's surgery So we're making back things smarter by putting in information that was not in the original file Might be in the person's head the person knows that three south is inpatient But we were able to tell back length that this is inpatient next And this time it only took 32 seconds because I talked less Let me just do this the fastest way begin conversion next next next So if I don't talk this only took three seconds Okay Backline did not understand all of your codes. Do you want to review new codes? Yes And you can see it's it's perfect. It understood all the specimens all the organisms all the antibiotics It understood some of the locations But I did not finish defining all of the locations because we don't need to do this on this phone call Any questions on that? The purpose of configuration is to find the data structure We're now defining the codes. We're making back things smart And now we have this new data file and this new data file has exactly the same data However, it's been reformatted into a language that who not will understand Any questions? I'm now going to go to excel And show you that file So here you see this file called test evd. That's the day today's time. That's the file that back then just made it made I'm going to open that file up And here you can see the who net data You can see the vitek data In who net structure So you you see exactly the same 28 isolates. Let me go to the bottom. There's 28 isolates here You can see the location you can see Here you can see the vitek organism name and you can see the who net organism name You can see it's gram positive gram negative You can see the antibiotic results But these are now using the who net codes The who net code is not superflexus in the who net code is sip So let me compare this is what the vitek data look like using the vitek language Lab id john smith patient id the vitek data with vitek structure These are now the vitek data with who net structure and it's exactly the same content But now in a way that who net will understand um I just can show you that let me go to who net And please prepare your questions. So i'm just going to do a quickie here I'm going to test and do open data entry open data file test.evd Click on view database. So here we are inside of who net looking at our vitek data So that's exactly that's the only purpose of back link I'm going to go continue as I'm going to try to open up. You know, that's fine. Let me close the excel Okay, and data entry open data file One thing I you know here is a reminder. You see the original data called vitek demo I'm going to try to open up that in who net And who net is saying I don't understand what this is So everything we did on this phone call was to basically allow who net to read the vitek data But it cannot read the vitek data in vitek format It had to read the vitek and who net format and that's exactly what we just did with back link Okay, it's close to time. There is time for a few more questions People often get confused the first time they do back link the second third time they do back link It's usually very very simple because they understand the concepts and they understand the screens So maybe uh Can I ask you one question? Of course, yes Uh, yeah Uh, are we going to change the original data in the way that who net? Uh, require that means for example Uh, especially the antibiotics Uh in panem, uh, for example who net abbreviates it as IMP right? If this abbreviation was No, no, okay. The entry to your question is that is exactly what we already did So let's see. So there's one thing I didn't show you click. I'm going to click an edit format Well, so first of all begin conversion. I did show you this So what you see here are the vitek antibiotics But using the who net codes So in entered your question, it has already done what you just asked So any panem is not the vitek code any panem is the who net code So the question is why was back link so smart? So let me click on edit format edit format I'm going to click on this option called codes and dates At the bottom you see there are four code dictionaries I already showed you the top two on the right hand screen. I'm going to click on view dictionary So this is the location dictionary that we made together This is the specimen dictionary that we made together I did not show you the organism dictionary or the antibiotic dictionary You asked about the antibiotics. So the antibiotic dictionary I told you that this existed, but I didn't show it to you. I'm showing it to you now Also, the vitek codes have changed over time. The vitek used to use these one two three letter codes Now vitek uses full name codes. So let me just find any panem So here you can see there's a middle column called local antibiotic code. So the vitek calls it imipenem But who net calls it ipm? So in entered a question. Yes, but it happened automatically Because this we went the same thing for organisms. I'm going to go to the organism dictionary So many many years ago. So vitek used to use six letter codes, you know strbov This was the old unix vitek one So they had so their code in in vitek one was strbov But who now calls it sbo? Those are the old codes the new codes are at the bottom And the vitek is strange. I don't know why they call it I don't know why they call it staff. Most people would call it staff lacoccus or just the letter s But the vitek current name is staff epidermidis. The who net code is scp So an enter your question that it's extremely important to convert it But backlink did it automatically because I gave this information to backlink many years ago Does that answer the question? Yes Maybe I don't know. Sorry. I'm getting lost while you are discussing the backlink configuration You already have the configuration or you already did it now I just did it right now. In fact it re-emphasizes. Hold on. Let me just go to my inbox. Um And let's see and sent an ng Um Hi all I am finishing my workshop with Ethiopia I will join You in a few minutes, okay and And dismiss dismiss and send. Okay. Well, okay, good And okay and Close the excel Don't say and and Just my email to send it out. Okay. So, um Get back to backlink Let me close. Let me go back to backlink. Okay. I'm gonna I'm deleting everything everything is now deleted So when you receive your who net and backlink, this is what you will see the configuration does not exist Backlink has a lot of knowledge built in that we are not yet taking advantage So basically this entire two hours. I'm going to repeat for you in basically two minutes. It's like a new format Ethiopia ebji vitec demo evd file structure Vitec two and that's where it does all the magic because then it realizes all of that mapping Let's call this evd. Let's call this exit Browse uh browse and I choose my vitec demo And I say test dot evd begin conversion And that's isolate one isolate two isolate three Okay, do you want to review the new codes? Not yet. I want to go back and I want to fix the date format Let me change this to to year month day year month day Modify the list of data fields testing date is also year month day. Okay save save exit Begin conversion isolate one the date is now fixed next next next Okay, review the new codes. Yes I it all I didn't delete I redid this but it already members the sputum and the catheterize urine Continue and that's it. I've just redone this entire two hour session Very quickly emphasizing how quick and easy the vitec is I talked a lot, but once you're familiar with these steps are very simple So in answer to question no, we did not give you the configuration ahead of time But we gave you a backlink that was very smart that understands vitec very well. So as soon as I said here As soon as I said vitec data That's where it automatically set up the data fields as you can see collection date mapping. That's where it automatically set up All of the organism dictionaries the antibiotic dictionaries So so backlink has done a lot of smart stuff behind the scenes Okay okay This file here, I guess the final thing to show you is I go to this pc who in that There is a configuration file here Called evd. That's the one that I just made And there are also these code dictionaries code dictionary I only made the location one. So um No, let me sort this alphabetically that would be better Right so these are the vitec code dictionary So all of that is so I'm going to go to this other folder called machines And here you see the antibiotic dictionary for biomech and microscan and the phoenix and all these other systems So backlink gives you all this information and it leverages it once you do your own configuration And then if I want to copy this to another computer I just simply I just simply take this file evd and the dictionaries and just copy them to the other computer We can talk about that on another call. How do you move things from one computer to another computer? You just need to know the name of the file and where the file is saved