MCRI figshare User Guide

Manual text content

File MCRI_figshare_User_Guide_2018-07-03.docx Author Luke Stevens DOI https://doi.org/10.25374/MCRI.6729197 MCRI figshare User Guide Blank Page MCRI_figshare_User_Guide_2018-07-03.docx Page 1 of 24 Contents Contents ...................................................................................................................... 1 1 Introduction to figshare ......................................................................................... 3 1.1 What is figshare? ............................................................................................. 3 1.2 Why are MCRI using figshare? ......................................................................... 4 1.2.1 The Problem ................................................................................................. 4 1.2.2 The Requirements ........................................................................................ 4 1.2.3 figshare as the Solution ................................................................................ 4 1.3 How are MCRI using figshare ........................................................................... 4 1.3.1 Research Project Data Repository................................................................. 4 1.3.2 What can you Store in the figshare Repository? ........................................... 5 1.3.3 Free to Use ................................................................................................... 5 1.3.4 Data Storage Location .................................................................................. 5 2 Accessing figshare .................................................................................................. 6 2.1 Get a User Account .......................................................................................... 6 2.2 Logging In ........................................................................................................ 6 2.2.1 First log in ..................................................................................................... 6 2.3 Basic Navigation .............................................................................................. 7 2.3.1 Top of Page Menu ........................................................................................ 7 2.3.2 MCRI figshare Site ........................................................................................ 7 2.3.3 My data ........................................................................................................ 8 3 Projects .................................................................................................................. 9 3.1 Projects You May Access ................................................................................. 9 3.2 Create a New Project ....................................................................................... 9 3.3 Edit a Project ................................................................................................. 11 3.4 Project Metadata ........................................................................................... 11 3.5 Add Other Users to a Project ......................................................................... 13 3.6 Publish a Project ............................................................................................ 14 4 Items .................................................................................................................... 16 MCRI_figshare_User_Guide_2018-07-03.docx Page 2 of 24 4.1 Add an Item ................................................................................................... 16 4.2 Edit an Item ................................................................................................... 17 4.3 Item Metadata............................................................................................... 18 4.4 Reserve a DOI ................................................................................................ 19 4.5 Publish an Item .............................................................................................. 20 4.5.1 Apply Embargo ........................................................................................... 20 4.5.2 Make file(s) confidential ............................................................................. 20 4.5.3 Generate private link .................................................................................. 20 4.6 DOI Versioning ............................................................................................... 22 5 Help and Support ................................................................................................. 23 5.1 figshare Knowledge Portal ............................................................................. 23 5.2 Contact .......................................................................................................... 23 6 Document History ................................................................................................ 23 MCRI_figshare_User_Guide_2018-07-03.docx Page 3 of 24 1 Introduction to figshare 1.1 What is figshare? fig share is an online repository where researchers can make all of their research outputs available in a citable, shareable and discoverable manner. fig share allows users to upload files of any format and enables them to be viewed in the browser so that any research output, from posters and presentations to datasets and code, can be disseminated in a way that the current scholarly publishing model does not allow. Published files hosted on figshare are issued with Digital Object Identifiers (DOIs) via DataCite through the California Digital Library. DOIs are persistent and so provide a permanent link to your research. You can usually find DOIs under the titles of published articles in journals. For more information visit https://figshare.com/ . MCRI_figshare_User_Guide_2018-07-03.docx Page 4 of 24 1.2 Why are MCRI using figshare? 1.2.1 The Problem Many researchers will be familiar with the difficulties that can arise when trying to discover information about other – and particularly older – research projects. Who was involved? Who can I ask about what was done? Are there datasets or documents like SOPs that could be helpful to a current project? Often answering such questions means locating some person that has sufficient permissions to dig through the project's directory in the Research Group's share drive, and then trying to make sense of whatever can be found there. This is a very inefficient process and can result in valuable knowledge being lost to MCRI as staff move on to other projects or leave the Institute. 1.2.2 The Requirements So the need for an archive of valuable MCRI research project outputs was identified. MCRI has a clear interest in identifying and managing responsibilities for research project data and ensuring the accessibility of project information. Researchers’ also have a clear interest in simplifying and standardising the archival of their research project data and project documentation and in promoting discoverability and (potentially) knowledge/data sharing. Increasingly, also, there is a move to make research data more open, as espoused in the FAIR data principles. See https://www.ands.org.au/working-with-data/fairdata . 1.2.3 fig share as the Solution fig share emerged as a potential solution for a variety of reasons:  Quicker to implement and more sustainable than an in-house development.  Simpler to set up and manage than off-the-shelf open source data repository software (e.g. Fedora, dSpace).  "fig share for Institutions" enables the project-centric model we sought.  All items published in fig share are assigned a permanent DOI. 1.3 How are MCRI using figshare 1.3.1 Research Project Data Repository Differently to most institutions! MCRI are using figshare as a repository for valuable outputs of our research projects. MCRI_figshare_User_Guide_2018-07-03.docx Page 5 of 24 In short, this means that all items (documents, datasets etc.) that you place in the repository must be associated with a specific "project", where the "project" is a record of the work activity performed in creating the items. Examples of "projects" in fig share include:  Research projects  A regular series of publications: CCCH Policy Brief Series  A container for documents relating to MCRI's fig share ! 1.3.2 What can you Store in the figshare Repository? Anything you like! Anything you have produced as part of your MCRI activities that you think is worth preserving or sharing can and should be uploaded into the repository. Examples are:  Published papers  Datasets and analysis code used for published papers  Important project documentation o Protocol o Ethics approval o Study manual o SOPs o Data dictionaries  Project datasets, raw data and cleaning scripts  Presentations and posters  Other published documents like fact sheets, reports  Images and charts Items can be published publically or confidentially. Confidential items receive a DOI and their metadata record is visible, but only users associated with the item's project are able to view the item (i.e. the file or files). 1.3.3 Free to Use There are no charges for using MCRI's fig share . 1.3.4 Data Storage Location The fig share web application is hosted by fig share using Amazon Web Services. However, the storage of items (i.e. uploaded documents, datasets etc.) is in the process of being migrated to and stored permanently MCRI infrastructure. Until this process is completed, no items (e.g. datasets) containing participant-identifying data may be uploaded to fig share , and all items uploaded require a review and approval via fig share 's "curation" workflow before becoming fully published. MCRI_figshare_User_Guide_2018-07-03.docx Page 6 of 24 2 Accessing figshare 2.1 Get a User Account Currently user accounts are created individually by fig share support. Contact luke.stevens@mcri.edu.au who will make the request on your behalf. If you have a number of people for whom user accounts are required it is appreciated if the requests can be made in a batch. User account requests are typically actioned overnight, Australian time. 2.2 Logging In Log in to fig share at https://mcri.figshare.com/ . Enter your fig share username and password. The Forgot password? link is there should you forget your password and need to reset it. 2.2.1 First log in The first time you go to log in to fig share after obtaining a user account you will need to use the Forgot password? link. MCRI_figshare_User_Guide_2018-07-03.docx Page 7 of 24 2.3 Basic Navigation 2.3.1 Top of Page Menu 1. fig share .com 2. MCRI fig share 3. Your projects and items 4. Search fig share .com 5. Your researcher profile 2.3.1.1 figshare.com Browse items on the public figshare.com site. 2.3.1.2 MCRI figshare Browse items in MCRI's figshare site. 2.3.1.3 My data Access your own items in MCRI's figshare site. 2.3.1.4 Search figshare.com Search items on the public figshare.com site. To search MCRI items click the MCRI logo and go to the search box in the main body of the page. 2.3.1.5 Your Profile Update your personal researcher profile and application settings. 2.3.2 MCRI figshare Site Selecting the MCRI logo in the page header takes you to the public facing Institution level page. Here you – and anyone – can search for items published in MCRI's fig share . Note: use the search field and filters in the main body of the page, not the search box in the page header (which searches in fig share .com). MCRI_figshare_User_Guide_2018-07-03.docx Page 8 of 24 2.3.3 My data The My data view is the main page you will see once you are logged in. You will see tabs at the top for viewing and creating new "items", "projects" and "collections", and a tab for any workflow related "activity" that is applicable to you. 2.3.3.1 My data: Items "Items" are the digital objects that you upload into the fig share repository. Items may be a single document or other type of electronic file, or a collection of related files that you wish to publish as a discrete set. All items you add to figshare must be contained within a "project". 2.3.3.2 Projects "Projects" are records of the work activity undertaken to creating items. Think of projects simply as the containers of items. Many projects in MCRI fig share will be research projects, but any activity that leads to valuable output stored in the repository can be created as a project. Examples of "projects" in fig share include:  Research projects  A regular series of publications: CCCH Policy Brief Series  A container for documents relating to MCRI's fig share ! See Projects for more information about creating and managing your fig share projects. 2.3.3.3 Collections "Collections" are groupings of published items from different projects. Items from different sources may be grouped in a collection, and the collection itself can be published and be assigned a DOI. Collections may also be private. 2.3.3.4 Activity You will probably not need to use the "Activity" tab. MCRI_figshare_User_Guide_2018-07-03.docx Page 9 of 24 3 Projects 3.1 Projects You May Access There are three levels of access that you may have to a project and its items: 0. Not associated You are not associated with the project directly. You may view only published items (metadata records of confidentially published items). 1. Viewer You have been granted permission to view the project and its contents without it published. Viewing includes unpublished and confidentially published items. 2. Collaborator Projects you have created, or where you have been given full access to view, edit and add items to a project, published or not. Accessing the projects tab will bring up a page showing projects from categories 1 and 2 above. You may use the Search and Filter options to refine the listing. Click on a project title to access it and view, edit or add items. 3.2 Create a New Project All documents, datasets – Items – uploaded to fig share must be associated with a project. That makes your first step in uploading items to find the project to which it should be added, or creating a new project record. Ideally a project will be created in fig share early in the life of a project , and appropriate members of the project team should be invited to collaborate on adding items. MCRI_figshare_User_Guide_2018-07-03.docx Page 10 of 24 To create a new project follow these steps: 1. Click + Create a new project on the Projects tab. 2. Enter a meaningful title and description (you are able to edit this later if needed). 3. Under Project Type you must select group and then the " Projects " group: This is important – you will not be able to save your project without doing this step as instructed. 4. With the " Projects " group selected a series of project-related metadata fields will be added to the form: Complete at least the mandatory fields (marked with the green circles) and as many of the other fields as possible (you may edit later). 5. At the foot of the form click Save changes . MCRI_figshare_User_Guide_2018-07-03.docx Page 11 of 24 3.3 Edit a Project A project may be edited at any time by users that have sufficient permissions. To edit a project follow these steps: 1. Click on the project title in the search results to open the project page. 2. If you have sufficient permissions you will see a cog icon and MANAGE to the right-hand side. Click MANAGE , and then Edit project details . 3. Make the edits you wish to make, then click Save changes at the foot of the form. 3.4 Project Metadata The available project-level metadata fields are: Metadata Field Description Title (required) A meaningful title of the project or activity. (Not just the study acronym.) Description Some useful descriptive text about the research project or activity. Funding Funding sources and grant numbers. Principal Investigator (required) Name of Principal Investigator. Research Group (required) Name of MCRI Research Group. Contact Person (required) Name of MCRI contact person. This may require occasional updates. HREC Reference Number(s) Ethics approval number(s). Ethics Approval Date Date of first Ethics approval. MCRI_figshare_User_Guide_2018-07-03.docx Page 12 of 24 Metadata Field Description Other Investigators Names of other investigators, MCRI and external. Collaborating Institutions Institutions of other investigators. Subject Areas Area of study, e.g. a disease or clinical area. Study Location Locations where research or activity took/will take place. E.g. RCH, Western Melbourne primary schools. Sampling Frame Description of the study population. Participant Numbers How many participants were/will be recruited. Can list by study arm and or by wave, indicating attrition. Year Commenced Four digit year. Year Completed Four digit year. Longitudinality Is there longitudinal data capture on the research participants? If so, describe the event schedule. Biological Samples Did/will the project collect biological samples from participants? If so, describe what samples collected, from whom, and when. Multimedia Collection Did/will the project capture video, audio or images from participants? If so, describe what kinds of data collected, from whom, and when. Ethics Re-application Date If known, when will Ethics re-application be required? Data Destruction Date What is the approximate end of the mandatory data retention period (7 years following the youngest participant turning 18 years old)? I.e. when can study dat a be destroyed? Data Destruction Requirements What will be required to destroy study data? E.g. deleting files from network storage, shredding of paper, physical destruction of data storage media? MCRI_figshare_User_Guide_2018-07-03.docx Page 13 of 24 Metadata Field Description Network Storage Location Full path of primary project net work file storage. Note full path , not a path containing a mapped drive letter! YES: \ \ storage \ mygroup \ myproject NO: G: \ myproject Project Website URL of study website. This can be a full site if your project has one or just a page within the Institutional website of MCRI or RCH. A place for people to go for further information. 3.5 Add Other Users to a Project Any fig share user may be added to your project, not just other MCRI fig share users. To search for and add a user to your project follow these steps: 1. Follow the Edit a Project steps to open the project editing screen. 2. Start typing the name, email address or ORCID of the person you wish to add. An auto-complete list will appear of possible matches. Hint 1: You may add more than one person at a time. Hint 2: Add a photo to your profile page to help people find you more easily. MCRI_figshare_User_Guide_2018-07-03.docx Page 14 of 24 3. Select the role that the user or users should have, Viewer or Collaborator: Viewer: May view the project, its metadata and items (including unpublished and confidential items) irrespective of whether the project is published. May not make edits. Collaborator: May make edits to the project and its items, and add notes. If you cannot find the person you would like to add in the auto-complete list, they will need to become a fig share user:  For MCRI staff, request a user account .  For external collaborators, send an invitation: 3.6 Publish a Project Once a project has at least one published item it can be published itself, becoming available to view (only) by anyone. The purpose of publishing projects is to make your research more easily discoverable – "findable" is the "F" of the FAIR data management principles ( https://www.nature.com/articles/sdata201618 ). A project that has a published item may be published via the option in the Manage list, or by ticking the box at the bottom of the Edit project form: MCRI_figshare_User_Guide_2018-07-03.docx Page 15 of 24 As it states there in the notes: once published, a project cannot be deleted. It can still be edited. MCRI_figshare_User_Guide_2018-07-03.docx Page 16 of 24 4 Items 4.1 Add an Item To create a new item first you must locate the appropriate project and ensure that you have permission to create new items for it. The steps for creating a new item are: 1. Navigate to the appropriate Project . 2. Click + Add new content , then + Create a new item in the dropdown. 3. Enter appropriate data into the item metadata fields and upload the file (or files). Fields marked with a green circle are required in order for an item to be published and assigned a DOI. See Item Metadata for more detail on each metadata field. 4. Click Save changes . NOTE: You cannot create a new item direct from the My data page because it will not then be associated with a project. You will receive a message about there being no storage quota available. MCRI_figshare_User_Guide_2018-07-03.docx Page 17 of 24 4.2 Edit an Item 1. Locate the item you wish to edit either within its project page or via an item search. If via a project page, click the cog icon, then select Edit item : If via a search or the My data page, click the pencil icon at the right of the item: 2. Make the changes you need in the metadata fields or to the item files and then click Save changes at the foot of the form. Changes may be cancelled without saving by clicking the X in the top-right corner of your screen, or by pressing Esc . MCRI_figshare_User_Guide_2018-07-03.docx Page 18 of 24 4.3 Item Metadata The item-level metadata fields are: Metadata Field Description Metadata record only Tick this box for items that are descriptive only – where you do not intend to ever upload a file. Title (required) A meaningful title for the item. Use something nicer to read than just the file name! Authors (required) Begin typing a name to see an au to - complete list. Select from the list or just press the Enter key to add an unrecognised name. Enter all applicable author names. Categories (required) Select a category from the list. For MCRI activities this is likely to be one or more of Biological Sciences, Health Sciences, Social Science, or Uncategorised. Item type Select your preferred item type from the list, e.g. for a document to publish select "Paper publication document". The "Fileset" option is available for cases where an item is a collec tion of a variety of item types. Keyword(s) (required) Begin typing a keyword to see an auto-complete list of previously used keywords. Select from the list or just press the Enter key to add an unrecognised term. Enter as may keywords as appropriate. D escription (required) Some useful descriptive text about the item within the context of the research project or activity. References Enter links for any applicable references. Funding Enter any applicable funders and or grant numbers (although these should already be recorded for the item's project). MCRI_figshare_User_Guide_2018-07-03.docx Page 19 of 24 Metadata Field Description Licence (required*) Select the most appropriate licence for your item. A licence is required for all published items but you may store files privately – unpublished – without specifying a licence. Use the (What's this?) link to find out more about each of the available options. See also https://creativecommons.org/licenses/ . Probably the most commonly used licences will be:  CC BY (Attribution)  CC BY-NC (Attribution, Non-Commercial)  RLT (e.g. data published confidentially where access must be requested and approved)  CC0: ("no rights reserved" – completely open) 4.4 Reserve a DOI Sometimes you may wish to know what an item's DOI will be before you finalise the item itself. Perhaps you want to include the DOI within a document, for example. In such cases you may create an item and request a DOI be reserved prior to uploading the final version of the item's file (or files).  The DOI text displayed can be extrapolated to give you the final DOI in its full form: 10.25374/MCRI.6729197  https://doi.org/10.25374/MCRI.6729197 While merely reserved, the DOI is not a valid URL. Only once the item is finally published will the DOI become active and lead to the item. MCRI_figshare_User_Guide_2018-07-03.docx Page 20 of 24 4.5 Publish an Item There are several options associated with publishing an item: All published items will be assigned a DOI. Remember to publish the project after its first item is published! 4.5.1 Apply Embargo Specify an embargo period or end date during which the item (or just the files) will be unavailable. 4.5.2 Make file(s) confidential Some files, e.g. study datasets – particularly of unit record data, should not be published publically, but are valuable outputs of your research activity and therefore should be archived and preserved in the repository. Such items should be published confidentially by selecting the "Make files confidential" option and entering an appropriate comment, e.g. directing to a website where data access information is located. The item metadata record is publically available (and hence the DOI is citable), but only users that are associated with the fig share project record have access to the item's file(s). 4.5.3 Generate private link Generating a private link enables anyone with the link (including non-fig share users) to access the item and its file(s). MCRI_figshare_User_Guide_2018-07-03.docx Page 21 of 24 The private link will provide access to the item before publication and/or to the files of an item published confidentially. 4.5.4 Publish! Once all required fields are completed, and any embargo period or confidentiality status is set appropriately, publish your item by ticking the box in the footer, then click Publish . 4.5.5 Curation Workflow When you publish an item it does not become public immediately. It requires a double check and approval from the MCRI fig share administrators. The administrators want to check that:  The item and item files do not contain any data or information that should not be made available in the form requested (e.g. confidential data in a dataset must only be published confidentially!)  The metadata entered for the item and project is relevant and sufficiently complete. MCRI_figshare_User_Guide_2018-07-03.docx Page 22 of 24 4.6 DOI Versioning A DOI is a permanent identifier of each item. It is, however, possible to make edits to already-published items, and to account for this there is scope for DOIs to include version information. Edit a published item in the usual manner (see Edit an Item ). You will then find that the item page indicates the presence of multiple versions, with each version having the version number appended to the DOI. Original DOI https://doi.org/10.25374/MCRI.6729197 V1 https://doi.org/10.25374/MCRI.6729197.v1 V2 https://doi.org/10.25374/MCRI.6729197.v2 MCRI_figshare_User_Guide_2018-07-03.docx Page 23 of 24 5 Help and Support 5.1 fig share Knowledge Portal Much more information on all things figshare is available via the fig share Knowledge Portal: https://knowledge.figshare.com/ . It contains various FAQs, information and tips, and a series of "How-To" guides. 5.2 Contact For more information about figshare, or for help and advice on using figshare at MCRI, contact : Luke Stevens Data Management Coordinator Clinical Epidemiology & Biostatistics ( CEBU ) Level 4, South Building Murdoch Children's Research Institute T x56552 (03 9345 6552) E luke.stevens@mcri.edu.au 6 Document History Document Author Version Comment MCRI_figshare_User_Guide_2018-07-03.docx Luke Stevens Initial version