OceanRep User Documentation
Help for all users (whether registered or not)
- 1. Quicksearch
- 2. Browsing
- 3. Searching
- 3.1 Simple versus advanced search
- 3.2 Text search fields
- 3.3 Lists of values
- 3.4 Tick boxes fields
- 3.5 Defining an advanced search
- 3.6 Results of searches
Help for registered users
- 4. Creating an account
- 5. Your work area: components
- 6. Your profile
- 6.1 Account details
- 6.2 Personal details
- 7. Saved searches
- 8. Manage deposits
- 8.1 Buttons new item and import items
- 8.2 Table of your eprints
- 9. Creating and depositing a new item
- 9.1 General considerations
- 9.2 Type
- 9.3 Details
- 9.4 Keywords
- 9.5 Upload file
- 9.6 Deposit to archive
- 10. Importing items
Help for all users (whether registered or not)
The quicksearch offers you the possibility to search quickly through the searchfields that are the most frequently ones: "author", "year", "title", "journal or publication" and "keywords".
Browsing is a good way to find papers (i.e. eprints) if you don't have a specific idea of what you're looking for. You do not have to create an account or login in order to browse. To browse the archive either select Browse from the navigation bar at the left side on the screen. Choose the category you wish to browse, i.e. author, research division, document type, year, subject. You will be presented with a list of sub-categories.
To access a paper, simply click on its reference in the display. On the abstract page, you can see documents attached to the eprint, and other details of the publications. You also see subjects and research affiliation for this eprint. Clicking on one of these will take you back to browsing by that subject or research affiliation, and finding all eprints related to this subject or research affiliation.
To export the list, select one of the export categories in the export roll-down menu at the top of the page.
3.1 Simple versus advanced search
Beside the quicksearch the archive offers two levels of search, simple and advanced, the advanced search allowing you to perform a finer-grained search. Access:
- Simple search using the search section on the search link in the navigation bar on the left side of the screen.
- Advanced search using the link on the left side of the simple search page.
The different types of search fields are described below.
3.2 Text search fields
To search by fields such as keywords, author, title, full text. These fields have a text entry area, a popup menu just to the left of it and a ? sign. Type your search term(s) into the box(es). Click on the ? sign to the right of a specific field for some help on what to enter in that field.
You can decide how the system will use your search terms by selecting from the roll-down menu on the right of the field.
- All of: The system will search for documents containing all the terms you typed.
- Any of: The system will search for documents containing either of the terms you typed.
Date: When searching with the date field, you can specify a single year or range of years that you are interested in:
- "2004-" retrieves only records with the years 2004 and afterwards.
- "2009-2010" retrieves only records with years between 2009 and 2010.
- "-2008" retrieves records with years 2008 and before.
3.3 Lists of values
For these fields, the search options are displayed as lists or as roll-down menus. You can select one or more values. If no value in the list or menu is selected, the system will not use that field to find eprints (i.e. it will retrieve eprints with any value of this field). If you select several values, you can decide how the system will use them by selecting from the roll-down menu on the right of the list:
- All of: The system will search for documents with all the values you selected
- Any of: The system will search for documents with either of the values you selected.
3.4 Tick boxes fields
Select the value(s) you wish to search for. If no box is ticked, the system will not use that field to find eprints (i.e. it will retrieve eprints with any value in this field).
If you tick several boxes, you can decide how the system will use them by selecting from the roll-down menu on the right of the field:
- All of: The system will search for eprints with all the boxes you selected
- Any of: The system will search for eprints with either of the boxes you selected.
3.5 Defining an advanced search
At the bottom of the advanced search page, two fields allow you to define your search.
Retrieved records must fulfill:
- All of these conditions: The system will search for eprints containing all your search options;
- Any of these conditions: The system will search for eprints containing any of your search options.
Order the results: allows you to order the search results by author’s name, document type, year etc.
3.6 Results of searches
On the screen displaying the results, you can:
- Access the document by clicking on the title
- Access directly the file(s) attached to the eprint
- Choose to refine search (for example to restrict your search using another field)
- Export results (choose the exporting format in the roll-down menu)
- Reorder the search results (for example by year instead of by author).
If you are registered and were logged in when starting the search, you have the additional possibility to save the search and be informed when new documents are deposited that fit that search (see section 6 below).
4. Creating an account
You need an OceanRep-account for certain services, such as depositing items or creating saved searches. Click on "Login" on the home page. Fill in your email address and your password of the datamanagement-platform. If you don't have this password just click on the word "Password" above the input fields and follow the instructions. The system will email you a computer generated password for your Ocean-Rep work area. You can modify this password under "my account" in the datamanagement-platform (see 5. below).
5. Your work area: components
To access your work area from the home page, click on login and enter your username and password. The system brings you by default to the manage deposits page. To logout of your work area, click on logout at the right of the navigation menu. If you have forgotten your password, click on reset and follow instructions.
In your work area, you can modify your profile, access your saved searches, manage your deposits and logout. These different components are explained in sections 6, 7 and 8 below.
6. Your profile
To complete your profile, click on the link in your work area. Your profile page shows your account details and your personal details.
6.1 Account details
- Make email visible to all: if you tick this box, your email address will be displayed on your public summary page.
- Hide email to all except repository administrators: if you tick this box, your email address will not be displayed on your public summary page.
6.2 Personal details
Some of this information will be associated with the documents you upload; some of it is purely for internal archive use. General information like your name, URL and e-mail address are public in some parts of the system, so it is inadvisable to put down a home address.
7. Saved searches
Registered users can save a search and receive an email notification when new items are deposited which fit that search. Login as a user, carry out a search, in the result page click on save search. The next screen advises you of a successfully stored search and let you choose several parameters for your search:
Once you have created saved searches, the list of their names shows on that page with buttons in front of each search, allowing you to: do search, view and modify settings, or remove.
8. Manage deposits
This page displays a table containing your eprints in Organic Eprints. If your workspace is empty, which will be the case when you first visit the page, you can start adding eprints by using the button New item (see 8. Creating and depositing a new item).
8.1 Buttons new items and import items
- New item button: to start depositing an item (see section 9).
- Import item button: to import eprints from other databases (see section 9)
8.2 Table of your eprints
Your eprints table contains different categories of eprints, displayed with different background colours. Eprints in the different categories can be displayed or hidden by ticking the boxes at the top of the table:
- User workarea: eprints you have started to enter, but have not submitted yet. These are not visible to users.
- Under review: eprints you have submitted and are under review by an editor. These are not visible to users.
- Live archive: eprints you have submitted and have been accepted by the editor. These are visible to users.
- Retired: your eprints that have been retired from the archive and are not visible to users or to you anymore.
To reorder the list of eprints: Click on the title of the column you want to sort by. Clicking a second time will reverse the order.
To modify the data displayed: use the add a new column roll-down menu at the bottom of the page to select the new column to be displayed. Remove a column by clicking on the X at the bottom of that column. Move columns to the right or the left by clicking on the arrows at the bottom of that column.
To perform some actions on the eprints displayed, use the icons to the right of that eprint:
- View item: to see the information entered for the eprint (the only possible action for your eprints which are already in the live archive)
- Destroy items: this is available only for eprints not yet submitted (i.e. in the category user work area). If you wish to delete one of your eprints under review or in the live archive, please contact the administrator and indicate the reasons.
- Edit item: to modify the information entered for the eprint. This is available only for eprint not yet submitted (i.e. in the category user work area). If you wish to modify one of your eprints under review or in the live archive, please contact your national editor or the administrator.
- Submit item: to submit the eprint for the archive. Once submitted, the eprint will be in the category under review. It will be reviewed by an editor, who will then transfer it to the live archive. If there are problems with the record (scope of the paper, information missing, file, etc.), the editor will contact you.
If you click on view item, you have the possibility to choose one of the tabs.
- Details shows you all the information entered for this eprint
- Summary shows what will be displayed to visitors when displaying the item
- Actions contains some features also available in the tabs or buttons (return item, delete item, move to repository, edit item) and interesting other features:
- new version: to submit a new version of this item. It will create an exact copy which you can then make changes to. This item and the new version will be linked.
- use as template: to create a new item using this item as a template. There will be no connection between the two items.
- return to work area: to send the eprint back to your work area.
- reindex item: do not use.
- Edit: to edit item (as available in several other places)
- Export: click on the format you wish to export to
- History: the actions which have been performed on this item.
9. Creating and depositing a new item
9.1 General considerations
- to start creating a new item, click on the button new item in your manage deposits page.
- The depositing process is divided into 5 stages with 5 forms to be filled (type, details, keywords, upload files, deposit to the archive), which show as buttons at the top of the screen. You can move between these by clicking on next/previous, or by clicking directly on the buttons. Always start with Type as this influences the information required at other stages. Once you've entered the relevant information, click on the button Next at the top of the entry page. If there are any omissions from the data, the system will give you details of what is wrong.
- If you start uploading a paper, you are not obliged to complete the process in one operation. The button Save for later on each of the 5 forms allows you to save the record and continue editing it later. Documents that you are in the process of uploading are in your manage deposits page, in the category user work area. To continue working on an item saved for later, go to your manage deposits area, and select the icon edit item to the right of the item title.
- To the right of each field, there is a ? sign with short help of what should be put in the field.
- Red stars indicate fields that are compulsory and need to be filled out.
Important: to create a new item from one of your existing items (either in the archive, or under review or in your user area), go to the original item in your manage deposits table, click on the icon "View Item" to the right of the title, go to the tab actions and use either: new version (to submit a new version of this item. It will create an exact copy which you can then make changes to. This item and the new version will be linked); or use as template (Create a new item using the item as a template. There will be no connection between the two items).
Types of input field you may see while completing the forms:
- Text boxes: Type the relevant information in, or copy and paste directly from your document.
- Checkboxes: Tick the most appropriate option.
- Roll-down menus: Select the most appropriate option.
- Tree lists: Browse the different levels of the tree by clicking on + signs, select one or more appropriate options from the list by clicking on add. You can choose as many options as you wish.
- Page ranges: Type the first page into the left-hand box and the last page in the right-hand box. If the range consists of a single page, enter the page number into the left-hand box, and leave the right-hand box empty.
Collection: Here you decide to which collection you attach your item:
- IFM-GEOMAR Archive (2004 et seq.): This archive contains the research output of the IFM-GEOMAR since the founding year 2004.
- Additional Archive (before 2004:IFM, GEOMAR, Non-IFM-GEOMAR): This archive offers the option to archive your research output as an IFM-GEOMAR scientist even if the work is from the time before your employment with IFM-GEOMAR.
Document Type: Select the one option on the list that best described your paper. The option you choose here will affect what information about your deposit the system will collect in later stages.
Fields that are common to most types of eprints
- Title: the title of your item.
- Abstract: A summary of the document content. If the document has a formal abstract then that is what should be entered here. No complicated text formatting is possible.
- Authors: Enter family name and given name in the format given on the first page of the document. If there are more than four authors, click on the button "More input rows". The email address is optional. Note that empty boxes are ignored. To remove names from a list just remove the name from the relevant boxes and leave it empty. Don't worry about leaving a blank box in the middle of the list; the system will “bunch up” the list. If there was an autofill because you entered the DOI, you need to delete the initials, click in the field of the family name and OceanRep gives you the matching author and fills out the field of the email address and the affiliation automatically.
- Corporate creators: Companies that are considered authors of the deposited document
- Refereed - whether this version of the work has been refereed or not.
- Status: whether your document has been published, is currently in the process of being published (in press), has been submitted for publications (submitted) or has not been previously published (unpublished).
- Official URL: if your document has been published online, please include the URL, with the initial http://. For Web products, this link is shown in the citation. Always give a direct link (the full URL) to the document, and not just to the hosting website.
- Year of publication: The date this document was published. For publications, this should be the publication date. The year is compulsory, whereas the month and day are optional.
- Date Type: The event to which the date applies, i.e. publication, submission, completion.
- DOI: For publications from commercial publishers, such as Science Direct, please use the persistent Digital Object Identifier (DOI) if available. The DOI has the form doi: long-number - a hyperlink URL for a DOI is constructed like this: http://dx.doi.org/long-number.
- Related URLs: If your deposit is part of a larger context that is available on-line, such as the homepage of a project or a conference, please enter the full URL of the relevant front page here (including the initial http://). To indicate a direct link to your document, use the field "Official URL", and not "Related URLs".
- Additional Affiliations: This relates to the project or organization that created the item. How to select the affiliation: Browse the list using the + signs, and select by clicking on the label add. The selected affiliation(s) shown before the complete tree, with the label remove, which allows you to remove that affiliation. If you think a research affiliation is missing, please contact the library staff.
- Contact Email Address: If the full-text is not available to the public, then requests to view the full-text will be sent to this email. The email address will not be made public.
Only a few fields are listed below. A help text is available by clicking on the "?" sign by each of the fields.
- ISSN - Unique code identifying a serial (example: 1055-0143; 0891-060X)
- ISBN - Unique code identifying a book (example: 1 871438 57 8, 067157826X)
Some additional information can be entered at the bottom of the screen. Click on + signs by the name of the field to see the content and help for each.
In the field "Keywords" you put in the keywords you would give to your doccument.
Subjects are selected by clicking on the label Add next to the subject. The selected subject(s) are shown above the complete tree, with the label Remove next to it, to allow you to remove that subject in case of mistake. Select at least one main subject category, and optionally other subject categories you think are appropriate for your submission, from the list.
- try to be as accurate as possible
- it is a good idea to select maximum 3 subjects in total, and to not just select lots of categories.
- if you are unsure, just pick the categories you are sure of.
- please carefully browse down the tree and do not systematically choose a subject at the higher level.
If you think there is a serious omission from the subject category list, please suggest a new category by contacting the library staff.
9.5 Upload file
You may attach one or several documents to your document. Each document is composed of one or several files and some additional information (e.g. restriction rights, type of file, etc.).
Important: Files should follow some rules. This includes:
- Do not use special characters in the file name (e.g. blanks, accents etc.)
- Choose a clear name for your file, preferably following the format "authorname-year-keyword.doc"
- Make sure that the document is citable, i.e. the file should contain name of author, year of publication, name of publication, place of publication/journal name, so that it can be quoted, if somebody prints it out and forgot where s/he got it from.
You should first select the tab of the type of file you wish to upload to your document:
- File: the simplest option, to load a separate file
- Zip file and Tar.gz file: to be used to load an archive/compressed file archive. For example, your paper may be stored in several separate files. This is often the case if your paper is stored in HTML format and contains figures. You can use a ZIP tool (available on all operating systems) or the “tar” and “compress” tools (commonly used on UNIX systems) to collect all those files into one compacted file, and then load that file.
- From URL: If your paper is up on the Web already, this option will let you specify the URL of that paper. The archive software will copy your paper from that Web site. You should be careful with this option, though; and read the “uploading from an existing Web site” section below.
Note: you can upload either all documents in the document, and then fill in the options for each of them, or upload a document, complete its options, then upload the next one, etc.
For file, zip, tar or gz
Once you are on one of these tabs, click the browse button, select the file and then click on upload. On the resulting screen, you may create additional documents, by using again browse and upload.
In many cases (e.g. PDF, Word, Postscript) one document is composed of only one file. However, you may upload several files in one document (e.g. an HTML document containing images). In this case, you should load first the first file in the document that a reader should be presented with, e.g. the .html file if your document is in HTML format (before entering the images), or the contents page if your document is spread over several uploaded several HTML documents. Then click on the link need to add additional files to this document? in the documents option, and you can then browse and upload more files for that document.
If you selected the tab from URL, enter the full URL of the first page of the actual document; do not just enter the URL of the Web site the document appears in or the URL of an index or contents page. See the section uploading from an existing Web site below.
For all documents: Once you have uploaded one or several documents, you will see, for each document uploaded, an icon representing the file(s) attached to it, and options of the document. Click on the link "show options" to the right of the icon if the options are not visible. Options needs to be filled in for each document attached to the eprint.
Options shown for each document
- Content: The content of this document (e.g. submitted preprint or published version, conference paper or presentation), as opposed to the format. Chose from the list or choose Other. The content type will be displayed together with the link to your document.
- Format: the file format of the document you have uploaded. We recommend using PDF or HTML format to ensure maximum accessibility. You may furthermore add a document in the source file format that your document was written in (e.g. Word, TeX, WordPerfect), which can be used for your future editing and writing.
- Visible to: allows you to choose the level of access restriction for this document. The categories are:
- Anyone: means access to anyone with internet access (default).
- Registered users only: access only to registered users at OceanRep.
- Repository staff only: access only to yourself and the archive staff. You can use this option for any additional source files that are archived only for your own future use. This is useful for the papers with stricter copyright requirements. Other users will see the information entered for the eprint (e.g. title, authors, summary), but will not be able to open the files attached. Official evaluators can be granted access to all the publications from specific organizations upon agreement with these organizations.
- License: Specifies an explicit license for this document (does not affect the access rights you grant). This repository allows Creative Commons licenses. Leave unspecified if this does not apply.
- Embargo expiry date: The date that a publisher- or sponsor-imposed embargo expires. On and after this date, this document will be made publicly accessible. Examples: 2010 - document made publicly accessible on 1st January 2010; 2010 June - document made publicly accessible on 1st June 2010; 2010 June 15 –document made publicly accessible on 15 June 2010.
- Language: primary language of the document
Do not forget to use Update document at the bottom of the document’s information to save the options. Delete document allows you to remove the document.
Convert document format: allows you to convert this specific file to another format and attach that new file to the document. Select the format you wish to convert it to and click Convert. Your old file will not be lost. The conversion will create a new document with file attached. Important: the options attached to the old document are not transferred and need to be filled in the new document.
When you're happy that you've uploaded all of the documents, it is recommended that you make sure that uploads have all worked, by trying to open the files, and to come back and fix anything that's amiss.
Notes on uploading from an existing website
When you give the archive a URL to retrieve your document from, the archive stores a copy of the file stored at that URL. If the URL is an HTML file, the archive will also copy the images associated with that HTML file, and other HTML files linked to it.
You must supply the URL of the first page of document itself: NOT the URL of the whole Web site, or the URL of any contents page listing multiple documents, index page or abstract page. Example: http://www.myinstitution.edu/~myhomepage/paper.html and NOT www.myinstitution.edu/~myhomepage/
In order to prevent the archive from trying to copy the whole World Wide Web by following every single link, some rules are applied when the system collects your document:
- Only files reached by “relative”' links are retrieved. For example, if the HTML contains a link to node1.html then node1.html will be copied. If the link points to http://somewebsite.edu/bar.html, then that URL will not be copied.
- Only files at the same depth or deeper in the Web site file hierarchy are retrieved. For example, if a link points to /index.html or ../index.html, the file will not be copied.
If something does go wrong, it's normally best to delete that file and try another uploading method.
9.6 Deposit to the archive
This is the final stage of the process, allowing you to submit an item, which will then be reviewed by an editor.
Before you go to the deposit stage, it is recommended that you carefully check that all information has been uploaded correctly at the different stages.
You should in particular check that the document files have been uploaded correctly, including any associated figures and links. If you spot mistakes, you can correct them on the relevant information page. If you're satisfied that everything is correct and has been uploaded correctly, click on deposit. You reach the deposit agreement page.
Any missing information or internal inconsistency within the information entered for the eprint is indicated in an orange field at the top of the page. You have to provide missing information and check inconsistencies before being able to deposit the eprint.
Once you have done that, and read, understood and complied with the agreement on that page, click on the Deposit item now button to deposit your document in the archive. It will then be put in the archive buffer.
The next screen confirms that your item has been deposited, and informs you that it will not appear on the public website until it has been checked by the library staff. It also displays all the forms as filled. A library staff member will then review the document and either transfer it to OceanRep or contact you for more information.
10. Importing items
The button Import items is available from your manage deposits page in your user workarea. It allows you to import information from external sources, such as Pubmed or DOI (Digital Object Identifier), into an document record. Different formats can be used: Pubmed ID, Pubmed XML, DOI system or XML. For details, see: http://www.eprints.org/software/training/users/depositing.php.
If you cannot find answers to your questions in this help, please contact the library staff.
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