NARRATOR: So here we go. The really important part, how you deposit. Your form -- yes? Could we save that questions 'til at the end? Okay, write it down and we'll have question and answer. Okay?
So there's four methods to deposit a manuscript that needs to be in compliance. This is a little foggy... it's not bad. The A, B, C, and D. Four methods. So Method A is a journal that will deposit the final version of the manuscript. In other words, that PDF that you click on, like if you're in PubMed and you see an MGet It button or publisher's and you click on that, that version is deposited by the journal. So, it would be nice to publish only in those journals then you won't have to jump through the hoops of making sure you comply. Okay. And there is a list and here's the URL. And if you download the version of this you'll see the URL and you can find out if the journal publishes, you know, deposits the final version, so you're fine. When you look at this list, for example, Blood is one of the journals that deposits. You need to look at the date that they started depositing it. If it was -- the date was after April 7, 2008, you're fine. If you're-- if it was-- if the date was did not fall into that, they published it-- this year they start depositing, the author or the PI needs to comply. So, those dates of when they started putting in the full text of the man-- the publication, it is very important. You just can't make the assumption. The other thing is and when we look at the...NIHMS system, when you go ahead and start depositing something, the system will say, 'You do not need to, the journal does it.' So, you can just stop right there. So, before it goes on any further, the system will let you know that you're off the hook. So, this is very -- something you need to be very careful of. That, often on a copyright agreement there'll be a little box that says, 'Would you like this manuscript to be deposited in open-access?' Or, deposited or you give us an agreement that we can post it on our webpage, anyone can click on it -- find that is in compliance but, there's usually a fee that they don't tell you about. So, when you check that, they will tack on to the publication fee anywhere from a $1,000 to $3,000. So, do not check that box because the policy, the NIH Public Access Policy, says you don't have to do that you just have to deposit a version, a peer-reviewed version. So, this -- I think everybody's aware of that -- all the authors and the PIs, not to check that box unless you have an extra $1,000 or $2,000 that they can tack on to the exorbitant fee they charge you for publishing your manuscript and the colors and the plates which is very expensive. These are some of the journal publishers that are involved in doing that.
Method C, this is the method that most people are going to -- most researchers, authors have to... will be using and that's the one where the author or the Principal Investigator or someone they've assigned to do that does the deposit. And D is similar to Method C but the journal deposits a version, a peer-reviewed version. They do it for... the author and it usually says in their instructions to the author that they will do this. Once they do that, the author or the Principal Investigator is not off the hook. They put some -- a version in there and then the person that they, it's usually the author or the Principal Investigator, they -- the publisher's indicated who NIH or who NIHMS (manuscript submission system) needs to notify to...approve the deposit. So, if you are supporting a faculty, you need to make them clearly aware of the fact that they need to approve, even if the journal does it in -- as Method D.
The other thing is, you see in the red, sometimes they're just going to put in the letter of the law, they'll follow it, that says the final peer-reviewed. That's even before any typos are corrected, anything like that some of the journals just put that in and it doesn't really look good. It looks like you are not speaking English sometimes because there may have been something that... the sentence wasn't constructed correctly and... the reviewer doesn't say, 'Well, this sentence isn't constructed well.' And that's the version that they put in which is what the policy says, the final peer-reviewed. So you need to make sure that what is in there, or whoever is assigned as the approver looks good, doesn't have a lot of typos or anything. You might have to fight with the journal on that because once they do it, they don't want to be bothered anymore.
So, what do you deposit? Journal articles only, that have been funded by an NIH grant, the final peer-reviewed. It's up to you. I have some researchers I've worked with that take the text file and take the images and insert them into the document and then create a PDF and that's what they upload. So, if you have a lot of time on your hands, you can do that. But, that's not what you you need to do.
The text part of the manuscript can be a .doc, a .txt, rich text format. So, any type -- any format like that. You also need to make sure that any tables or images or supplemental data that are not embedded in the text, but are part of the publication those need to be submitted as well. Okay? Again, there's the magic date, April 7, 2008 forward.
Don't try to deposit book chapters, books. Book chapters are not peer-reviewed. Again, non peer-reviewed articles, letters to the editor, commentary, conference proceedings -- they don't want that. And any dissertations. Even though a faculty member may have a graduate student working on their dissertation and they're getting funded, part of their salary's getting funded by their NIH grant, that doesn't need to be deposited. It's not peer-reviewed even though the dissertation committee may look at it and make comments, it's not what's considered peer-reviewed. So, it gets you off the hook. Again, upon acceptance for publication, the 12 months is the embargo. It doesn't mean you have 12 months, however, there are instances when, 'Uh oh... we forgot to deposit.' There's no reason you can't do it at point of need but it's really better to do it when you still, when the P.I., or you have access to that manuscript. I've had cases where it's gone somewhere and no one can find it. The person who actually has that version has left the lab or left the University and it's so difficult to track them down or they haven't even kept it. So, make -- so it's best to do it at the point when you have access to the document.
Okay, there's four steps, and I'm going to show you how this works but, step 1 is setting up the manuscript. Submitting all the manuscript files -- everything that's involved in the publication. Approving the deposit so that a PMC can be assigned. And then, there's... approving on the web, and I'll show you what that looks like. So, it's the approver. If you are supporting somebody and you deposit it, I would be loathe to make myself the approver because I don't understand the science of the text or if the images didn't look good. So, really puts the onus on either one of the authors or the Principal Investigator to approve the submission.
So, here's what it looks like, the manuscript submission system, and there's four portals that you click on to login. So, the first is for NIH or eRA Commons. You can do it through that portal. The second is the publisher. This is where the journals go. They have access to that part of the deposit system. Howard Hughes has their own portal to deposit for their researchers.
And then the my NCBI. My NCBI is a place for anyone who's been assigned by a NIH grantee to do this for them. So, I'll show you how that works. So, once you get into the system by one of those four portals, you'll get an information screen which is hopefully covered in this presentation. And you just click Continue. And here's how you start. You click on submit a new manuscript. The first thing you put in is the journal name. And there's a feed that as you type, start typing a journal name it will prompt you and it'll fill it in for you. If you typed lower case, that's fine you don't have to type you don't have capitals or anything. They will put it in according to what the system wants. Then you put the manuscript title, the title of the manuscript and you click next to find the grant that you want to assign to this deposit. And you can do that in two ways. You can put in the author's first and last name. Or if you know the grant number -- this is sort of tricky. Sometimes you put in a number and you know it's a grant number but it doesn't quite come up so it's funny how the -- what the system will accept is a grant number. So, if you have the first and last name that's probably the best way. And you click this search button and you get a list of the grant holder, this NIH grantee, what grants they have. And you can select-- there are often-- looks like the same grant you can see and then there's .02, so this is a second iteration. It got refunded and refunded. It's up to you.
It's probably fine to take the first iteration to cover all the deposits even, if the publication even if the publication was -- came out of the 05 version of the grant. As long as the first, you know, NIH grant ROKR08 et cetera, et cetera, et cetera is acknowledged. And then you hit next manuscript info. This is the screen that allows you to upload all the different parts of the manuscript. So, the first thing is the text file, and if you have a PDF, if you've had time to make a PDF out of everything you just upload that. Because it should indicate figure one figure two and the figures should be in there, so that-- that's fine. You just find that and just upload it. Then there's the figures, the tables and the supplemental data. Trick is -- that you have to say in the line under label, you have to say, figure one. If you don't it will tell you 'You didn't label that file.' You can do figure or Fig. 1 and Fig. 2, whatever, and then the table is the same thing. You have to label it as Table 1, Table 2, Table 3. And if you have more than one figure you see at the bottom, in blue there's a little plus where you can click the plus it'll give you another line for additional figures or additional tables. And even if there's more than one supplemental data, you would just click the add and it would give you another line. Again, you have to label it supplemental data. Okay?
This is what it looks like. You can see here is several figures, five figures and two tables, and they have to be labeled. And when you do, when you've uploaded everything, you'll see this window that will show you that the system is uploading all those files that you have put in this table. You have to wait until it's all done, otherwise it's not going to work.
Upload files and this is what it looks like when everything has been uploaded. You'll get a '100% has been put into the NIHMS system.' And this is what it looks like after everything's been loaded. There's a PDF version, as you can see on the top. You could click on it and look at it. There's other things you have to make choices here on this screen. Once you do this, I think it's amazing how quickly that PDF is created. It's very much in real time. Don't-- you know, hit the reload button because you'll see a message saying, 'This may take awhile.' The system will refresh automatically every five seconds until everything is put in. So just give it a chance, especially if it's a real busy time. A lot of people are scrambling to get everything in. So here is where you can make the embargo. Anywhere from immediately to 12 months. So you can make a judgment call. If it's been out there for a year or so, you can say 'immediate' because the journal has already had a version out there. Or if it's been 6 months you might say '6 months.' So you can make a judgment call. If you've just received acceptance I would put '12 months' to be safe. You don't want to have any trouble with the journal.
And here's everything -- everything has been -- the choices have all been made. If you don't check any of those boxes, the system will say 'You need to check whatever.' So the system really gives you a good helping hand. And you hit the 'Approve' button. I want to go back here and show you. Who is the approver? The approver is the grant that we assigned, but, especially if it's a center grant or a training grant, the PI is gonna maybe not know anything about that publication. They're not an author on it. You can opt to select somebody else. You click the second button, you put in the person's first, last name and the email address. So it can be somebody other than the PI. If you want to do it, if you're support staff, that's up to you. And this is what it says, 'Awaiting author approval.' It's at this point that they need to get someone who has been designated to approve the deposit. So here you go.
On the second screen, the screen where you put in the journal name and the manuscript. There was a NIHMS number, if you wanna go back, I can show that to you. So you get that NIHMS ID number pretty much right away. That's the number you can use for compliance. So here it is. See, it's got all the journal information, and the NIHMS ID. The NIHMS ID shows that you have started the process, and you're in compliance. So if you need to grab that, you can grab that at any point because it's always there, even on the last screen where it says 'Waiting.' So it's up there, and you can just grab that off there. So, here it is. Approval goes to whoever you have assigned to approve it. They need to review the PDF. They need to see if it looks good.
If the images look good-- any problem with it, they can say they don't approve, and it will go back and you can make whatever corrections. So here is a PDF, this is what it looks like. What's going to be loaded into PubMed Central will not be that first page. This is for the person who's approving it to make sure it's the correct journal name, it's the correct grant, all those things. As long as everything there is right, when you hit 'Approve,' that's what is going to be put into the system.
And then here's the PDF, the text file. There's an online version of approval, where they can click on that and go online and make any kind of changes here. If they want to request corrections, not necessarily the whole version that's been deposited, they click on 'Request Corrections' or 'Approve' if everything looks good. Whichever. And the corrections are done just like a page proof. Here's what that looks like. So you click on 'Request Corrections,' you get this page and then you put in where-- on what sentence-- what needs to be corrected. And anyone who's gotten page proofs understands how you say, 'On line 35, please put in this word instead of that word.' You can just do several corrections. You can add another request for corrections. There can be different lines where you request some kind of-- spelling is wrong or something. So it could be right here.
So after approval, you have the NIHMS ID. So if you're doing it for somebody, you want to let them know, this is the NIHMS ID number for this deposit. And make sure, if you are the approver, that you don't delete any messages that come from NIHMS. Because that's the message that says-- let's you go in and approve. They send you three -- they send the approver three messages. It's never moved out of the system, it's just put in hold. So if they forget, and then realize that they haven't approved it, they can go in either through eRa Commons or myNCBI and put the NIHMS number in and then they just hit approve. It'll get moved back through the system for a PubMed Central ID to be assigned. Okay, so it's never-- you don't totally lose it.
So here is what one of the MEDLINE records looks like. You can see there's a PMID-- and I'm going to talk about the difference between PMID and a PMCID. So you can see, this has a PMCID... right there. That shows compliance. And If you click on that link up there that says 'Free in PubMed Central,' you're going to pull up the PDF that the NIHMS system has created from all those files that had been deposited. And you can see, because of copyright that at the bottom it says the final final version of this is...at the Nature Genetics site. So, it's letting you know that this isn't the final version. Copyright belongs to the journal. You can see at the side, if someone prints this out, that it says that it's the manuscript version. So it may not be the same version as they get when they go to the journal and click on PDF, which is going to have the running title and all that information that they can't put in here. Here's the PMCID and the NIHMS ID, both of them. And it also has this 'other articles' that are citing this deposited article. So you can click on that. Those are articles that are in MEDLINE. They're not necessarily in another journal that's not in MEDLINE.
This one has a PMC. You can see the embargo 'Available on--' it's been embargoed. You see there's no PubMed Central on this one. because they can't release it until that date.