DOI-Genres
Steffen Lindek
Version 1.0, 01/06/00
BioImage DOI Genres
This document describes the work done in May 2000 to define and describe DOI Genres for the BioImage database.
About BioImage
BioImage () is a database for microscopy images of biological specimens and their complete description. The metadata covers five areas:
• organizational information (authors, affiliations, references, etc.),
• sample preparation (preparation steps and their biochemical and physical parameters),
• biological specimen (taxonomic information, etc.),
• data (file location, format and size, etc.), and
• instrumentation (microscopes, their components, and the settings for the data acquisition).
The data documented in the BioImage database is recorded with a broad spectrum of microscopy techniques: two-dimensional atomic force microscopy images, three-dimensional density distributions and isosurfaces reconstructed from electron microscopy data, videos, and four-dimensional series recorded with confocal light microscopes. Since each of these techniques has its specific applications, the observed biological samples range from entire organisms to macromolecules.
The first step of the project documented here was to identify entities in the database that qualify for a DOI. Although the DOI can be extended to apply to all kind of entities (such as microscopes), the selection was restricted to intellectual property relating to publications. Therefore, the relevant entities are the study (this corresponds to a journal article), the dataset (an individual experiment), and the file (data file (microscopy data) and image file (images derived from the data)).
The approach, which reflects the concept of DOIs for print publications, was to take the hierarchy of entities in the BioImage database (study, dataset, and file) and to see the problem as functional granularity issue. The central entity is the study, which has to be tagged with a DOI, and the other entities at a lower level can be identified by a DOI if necessary.
However, this does not take into account that the type of entity varies within the hierarchy. Whereas the study and the dataset are print-publication-like compilations of scientific material (texts, figures, etc.), the data files and figures (or images) belong to a more basic type of data. Although the latter are also associated with textual data (a title or a description), they basically consist of one homogeneous file. The attributes that are required to describe the two types of entity are thus different. The metadata for the study and the dataset is similar to the metadata described in the DOI-X journal article Genre. For files, attributes like format, size and compression are more relevant. Therefore two DOI Genres have to be introduced: DOI-E for electronic publications like BioImage studies and DOI-I for images and image data. Whereas the first Genre, which is currently BioImage-specific, may turn out to be an extension of the DOI-X for print publications, the latter Genre is very general and applies to all kind of images (even non-digital material like paintings). Therefore two tasks that result from the development presented here are to investigate (a) whether DOI-E, DOI-X and the DOI for eBooks can be unified and (b) how the DOI-I has to be extended to cope with image data in other subject areas (e.g. arts).
In summary, the Genre derivation can be decomposed into three steps (that will be called views later in the document):
|Identification of the entities in the database that qualify for a|What should be identified by a DOI? |
|DOI, and classification according to their relationship. |Is one entity a sub-entity of another or is it independent? |
|Correlation of the entities with entities in other DOI Genres. |To which other entity (or entities) does a new entity correspond?|
|Classification of the entities according to their type, and |Which of the entities are similar? What metadata is relevant for |
|definition of a DOI Genre for each distinct type. |a type of entity? |
The fact that the BioImage database has a deeply structured and complex model had both advantages and disadvantages. On one hand, it would have been easier to derive a Genre (DOI-I) from a flatter repository that just contains annotated images. On the other hand, the hierarchy of BioImage entities is well defined, and extracting a hierarchy (step 1) was therefore not a problem. In addition, the multileveled structure allows a more thorough analysis of the entire task and is more helpful for designing a general strategy for deriving DOI Genres.
1. The structure of the BioImage database
The BioImage database is structured hierarchically: A submission is classified as study. It consists of one or more experiments (termed datasets), which were done to produce microscopy data (files). From these raw files, images (or figures) can be derived. These images are copies or versions of the data, characterized by a format (jpeg, tiff, etc.). In that sense, the relation between an image and its data is the same as the relation between a PDF or HTML version of an article and the article as such. Also the printed version of the article is only a version of the generic article because the content is adapted to the paper medium which may led to a reduction – but we will not discuss this further here.
Many other databases only contain images, no generic data files. One reason for this is that the generic or original data is not in digital form (a typical example for this are museum databases with photographs of traditional, i.e. non-digital art). And many of them do not have containers such as studies and datasets. They are just flat image collections in which grouping is realized through the attributes of the images rather than through top-level entities with their own metadata.
There are three views or steps on which one can base the analysis that leads to the definition of a DOI genre:
A) Independent hierarchy
B) Content-related hierarchy
C) Entity-related classification
A) In a first step, the hierarchy of BioImage entities can be considered to be independent from other hierarchies, the root for each of the hierarchies being the publisher (Table 1). The database then corresponds to a journal or a book.
Table 1. BioImage and its creations – A table to visualize the parallels between printed publications and BioImage entities.
|Books |Journals |BioImage |Images |
|Publisher [PUBID – to be |Publisher [PUBID – to be |Database Provider [DBPID – to |Database Provider / Publisher |
|defined] |defined] |be defined] |[ID – to be defined] |
|Book [ISBN] |Serial/Journal [ISSN] |Database [DBID – to be defined]|Resource [ResID – to be |
| | | |defined] |
|Volume |Volume [Number] |Study [BioImage ID/DOI] |Image [DOI] |
|Section |Issue [Number] |Dataset [BioImage ID/DOI] |Part (Sequence of video, part |
| | | |of composed image) [DOI] |
|Chapter |Article [DOI] |File/Data [BioImage ID/DOI] |Channel (in multichannel image)|
| | | |[DOI] |
|Item (Paragraph, Figure, |Section (Header, Abstract, |Image [BioImage ID/DOI] | |
|Caption) |Introduction, Figure, Caption) | | |
The item in square brackets is the identifier. The terms figure and image are equivalent. The bold setting emphasizes that these are creations that can be treated independently (4th column).
Note the correspondence between the citation formats:
Journal article: P. Miller et al., J. Struct. Biol. 22 (4), 277 (1987).
BioImage file: P. Miller et al., BioImage 22 (4), 277 (1987). [file 277 in dataset 4 in study 22]
BioImage dataset: P. Miller et al., BioImage 22 (4) (1987). [dataset 4 in study 22]
BioImage study: P. Miller et al., BioImage 22 (1987). [study 22]
Image: P. Miller et al., ImageDB 22 (4), 277 (1987). [channel 277 in part 4 in image 22]
Generic: Authors, DatabaseName TopLevelID (SecondLevelID), ItemID (Year).
B) A more elaborated view relates the elements within the hierarchies to each other. In the present case is based on the functional identity and content-specific equivalence of BioImage studies and journal articles (Table 2).
Table 2. BioImage and its creations – An enhanced view.
|Books |Edited Books |Journals |BioImage |Images |
|Publisher [PUBID – to be |Publisher [PUBID – to be |Publisher [PUBID – to be |Database Provider [DBPID |Database Provider / |
|defined] |defined] |defined] |– to be defined] |Publisher [ID – to be |
| | | | |defined] |
| |Book [ISBN] |Serial/Journal [ISSN] |Database [DBID – to be |Resource [ResID – to be |
| | | |defined] |defined] |
| |Volume |Volume [Number] | | |
| |Section |Issue [Number] | | |
|Book [ISBN] |Chapter |Article [DOI] |Study [BioImage ID/DOI] |Image [DOI] |
|Volume / Section | | |Dataset [BioImage ID/DOI]| |
|Chapter | | | | |
|Item (Paragraph, Figure, |Item (Paragraph, Figure, |Section (Header, |Section (Abstract, File, |Part (Sequence of video, |
|Caption) |Caption) |Abstract, Introduction, |Image, Material & |part of composed image) |
| | |Figure, Caption) |Methods) |[DOI] |
| | | | |Channel (in multichannel |
| | | | |image) [DOI] |
The item in square brackets is the identifier. The terms figure and image are equivalent. The bold setting emphasizes that these are creations that can be treated independently (5th column).
This corresponds to a flat citation format (without enumeration of top-level and second-level containers, which are not required for BioImage anyway, since the file ID is a global identifier, unlike the page number, which is restricted to the printed item):
BioImage file: P. Miller et al., BioImage, File 277 (1987). [file 277]
BioImage dataset: P. Miller et al., BioImage, Dataset 4 (1987). [dataset 4]
BioImage study: P. Miller et al., BioImage, Study 22 (1987). [study 22]
Image: P. Miller et al., ImageDB, Image 22 (1987). [image 22]
Generic: Authors, DatabaseName, ItemName ItemID (Year).
C) The third view emphasizes the difference between files and images on one hand, publication entities (printed or electronic) on the other hand (Table 3).
Table 3. BioImage and its creations – The complete view.
|Books |Edited Books |Journals |BioImage |Files/Images |
|Publisher [PUBID – to be |Publisher [PUBID – to be |Publisher [PUBID – to be |Database Provider [DBPID |Database Provider / |
|defined] |defined] |defined] |– to be defined] |Publisher [ID – to be |
| | | | |defined] |
| |Book [ISBN] |Serial/Journal [ISSN] |Database [DBID – to be |Resource [ResID – to be |
| | | |defined] |defined] |
| |Volume |Volume [Number] | | |
| |Section |Issue [Number] | | |
|Book [ISBN] |Chapter |Article [DOI] |Study [BioImage ID/DOI] |File/Image [DOI] |
|Volume / Section | | |Dataset [BioImage ID/DOI]|Part (Sequence of video, |
| | | | |part of composed image) |
| | | | |[DOI] |
|Chapter | | | |Channel (in multichannel |
| | | | |image) [DOI] |
|Item (Paragraph, Figure, |Item (Paragraph, Figure, |Section (Header, |Section (Abstract, File, | |
|Caption) |Caption) |Abstract, Introduction, |Image, Material & | |
| | |Figure, Caption) |Methods) | |
The item in square brackets is the identifier. The terms figure and image are equivalent. The bold setting emphasizes that these are creations that can be treated independently (5th column).
Although the view is not important for the database (model), it is relevant for the DOI genre. The general XML-DTD model that will be presented later is based on the first view (Table 1). It therefore uses the mandatory CrossRef element enumeration. If it were based on another view, this element would have to be optional. However, this requires the database to allow direct access to its creations though a global identifier, and this is clearly a functional granularity issue. The two XML-DTDs for DOI-E and DOI-I that will be presented are refinements of the general XML-DTD model and reflect the third view.
Before presenting the DOI-Genre-to-kernel maps and the XML-DTDs, the relevant elements of the BioImage database are discussed in more detail.
2. The elements of the BioImage DOI Genre
Study
A study is a submission to the BioImage database. It is now defined as a one-to-one equivalent to a journal article. By extension, any group of experiments that forms a complete investigation is also a study, even if there is no corresponding publication (the presence of a printed publication is preferred for database management, since it is a quality criterion that would have to be replaced by some internal assessment).
Dataset
A dataset is a set of microscopy data files acquired during an individual experiment. While an individual experiment usually does not form a scientifically complete investigation, this does not a priori exclude the submission of individual datasets to BioImage (in this case, a study is defined that forms an umbrella to a single dataset).
File/Data
A file is a microscopy data file that comes more or less directly from the microscope. For some instruments this is just a matrix of numbers encoding the intensity of a pixel; for others the data is formatted into a proprietary or general format (e.g. TIFF). It is usually not an image but a file that is used to generate images. The original video is also microscopy data file.
Image
An image is an image file that has been created from the microscopy data. Although an image may be identical to the data itself in some cases, an image is generally only one view of the data (there is an infinite number of images that can be created from a single data file by varying the parameters). By extension, the term image also applies to videos generated from the original video.
NB: Images are not stored as own entity in the BioImage database. They are currently treated as data files (i.e. BioImage does not differentiate between image files and microscopy data files).
For the basic view, data files and images are treated like studies and datasets. However, table 3 suggests that there is a fundamental difference between these types of intellectual property. Whereas BioImage studies and datasets resemble electronic publications due to their compilation-like character, data files and images form a different type of intellectual property. Therefore, in a further step, two different DOI genres are introduced: DOI-E for electronic publications (and BioImage studies and datasets qualify for this DOI as well as electronic books or journals; maybe this will turn out to be simply the extended DOI-X) and DOI-I for images.
Metadata
An image in the BioImage database has the following descriptors. These can be used to define the image metadata set stored with the DOI.
ID identifier
DOI identifier
File_location identifier (holds the URL submitted to the DOI metadata database)
Dataset role (link to the dataset whose constituent it is)
Step role (link to recording)
File_type form (currently video or non-video for database technical reasons)
Description label
Preview identifier (holds the URL or at least the name of a thumbnail image)
Contact role (link to copyright holder)
File_format role (link to file format (format name, extension))
File_size quantity
Process_quality role (link to processing quality information)
Compression_alg label
Compression_degree quantity
The underlying microscopy data has the following descriptors:
Content label (kind of information that is in the channel, e.g. density, height…)
Depth quantity (bits/pixel)
Label identifier (intra-file, not study or database wide)
Bio_content role (link to visible biological feature)
Axis_size (x,y,z,t) quantity
Axis_unit (x,y,z,t) label
Spacing (x,y,z,t) quantity
Resolution (x,y,z,t) quantity
Videos have the following descriptors (just the interesting ones; some of them are defined for chunks and strata, which are Informix-specific subdivisions of the video):
Title label
Event role (link to event, since subdividing is event dependent)
Specimen role (link to specimen, since they may be visible at different times)
Standard role (link to standard (name, framerate, linesperframe, visiblelines))
Capturerate quantity
Duration quantity
Numachannels quantity
When quantity
3. BioImage entities and printed publications
The entities in the BioImage database are closely related to bibliographical references. The references to printed publications can be classified as follows:
• primary reference – the publication that corresponds to the study (there is a one to one correspondence of studies and printed papers).
• secondary reference – the other publications/studies whose datasets are reused in the given study.
• tertiary reference – the other publications/studies that use datasets submitted with the given study.
• quaternary reference – the publications that are cited for steps, specimens, etc.
For a given reference, there are thus four types of studies that can be found in the BioImage database:
• primary study – the study that corresponds to the publication.
• secondary study – the other studies whose datasets are reused in the given publication.
• tertiary study – the other studies that use datasets submitted with the given publication.
• quaternary study – the studies that cite the given publication for steps, specimens, etc.
A dataset is an entity that describes a biological experiment. It is thus content-defined and does not correspond to a fixed part of a printed article. Files associated with a dataset are either microscopy data files or supplemental files (images, tables) that do not result directly from a data acquisition process. While there is no print-publication equivalent to microscopy data files, supplemental files correspond to figures in a printed article. In full-text bibliographical databases, it is therefore desirable to have a link from the individual figures published in the article to their counterpart in the BioImage database. However, this depends on the level of granularity that is implemented by the publishers.
Table 4. Journal article figures and corresponding BioImage files
DOI P – Publisher DOI; DOI B – BioImage DOI
|Journal Article (ID = 7) |BioImage Study (ID = 1) |
|Fig. 1 |File (video) 1 of dataset 1 (DOI B/111) |
|Figure composed of three frames of a video (DOI P/71) |Suppl. file 1 of dataset 1 |
|Fig. 2 |Files 1 and 2 of dataset 2 (DOI B/121, B/122) |
|Figure composed of 4 images from two experiments (DOI P/72) |Files 1 and 2 of dataset 3 (DOI B/131, B/132) |
| |Suppl. file 1 of dataset 2 |
| |Suppl. file 1 of dataset 3 |
|Fig. 3 |Suppl. file 2 of dataset 2 |
|Table for experiment 2 (DOI P/73) | |
|Fig. 4 |File 1 of dataset 2 (DOI B/121) |
|Figure composed of two images from two experiments (DOI P/74); |File 7 of dataset 9 of study 3 (DOI B/397) |
|Fig. 4a is derived from the same file as Fig. 2 (i.e. DOI |Suppl. file 3 of dataset 2 |
|B/121); Fig. 4b was submitted with a previous publication to the| |
|BioImage database | |
| |1 study, 3 datasets, 5 files, 4 suppl. files |
| |plus any other data not published in the article due to lack of |
| |space |
Some topics need further attention:
• The files have a BioImage DOI (B/…); the supporting files should be identified by the publisher (P/…). Alternatively a BioImage DOI can be used for them.
• The publisher should provide the possibility to link their paper to the BioImage study and the figures to the datasets and files. For composed figures (e.g. Fig. 4) the individual images should be linked to the corresponding BioImage database files.
4. DOIs for customized items
DOIs identify creations (in BioImage these are currently files, datasets, and studies). Whereas the raw microscopy data files (the original or generic data) never change, processed data, supplemental files, datasets and studies mav be subject to updates or corrections (which is the reason for the introduction of a version attribute for datasets and studies in the BioImage database). This situation does not differ from what the publishers of printed publications, who are a major player in the DOI business, are confronted to. The situation for e-publishers, however, can be completely different if they do not only deal with stable documents, but also allow the retrieval of customized items. Then, every copy a user derives from an original document is unique.
One example for this arises from the use of VIDOS, a tool that allows the customization of videos and the subsequent download of the files from the BioImage server. The user chooses a three-dimensional (temporal and spatial) frame in the video, selects further parameters such as the frame rate, the file format and the compression; his video is then created on the server and transferred to his computer. There is little chance that two users will pick exactly the same parameters, and the videos will therefore all be different. While the original is identified by a DOI, it is a matter of functional granularity whether the derived files should be tagged by the same DOI or should receive a new identifier.
Identifying the copies by a DOI is not an issue if the only purpose of DOIs is to allow online access to the item (through the handle system), since the downloaded video will not be stored in a place where it is freely accessible (although the BioImage server may store the video for whatever reason). However, another purpose of the DOI is to allow tracking the video through the internet. While this is currently not implemented because the DOI cannot be attached permanently to the item it identifies, this will definitely be a future use of the DOI. Therefore it is important to tag the derived data files with a DOI, and the issue is to define a structure for it.
Another example for such use are three-dimensional (confocal) data sets, which the user can view from different angles. Each two-dimensional projection that is calculated should be identified by a DOI. Obviously, screenshots taken be the user in his browser cannot be tagged by a DOI.
It was suggested that BioImage DOIs should have the structure X000 where X stands for the type of item (study (S), dataset (D), file (F), etc.) and 000 for its ID. 000 stands for a number of any length, not just three digits. 10 digits is the length of a 4-byte integer that is currently used for the IDs in the database.
The timestamp of the customization (YYYYMMDDHHMMSS) and the IP number of the server that performs the operation could extend the original's DOI (provided there is no parallel processing on the server). In this case we would have the following suffix string:
F0000000000-YYYYMMDDHHMMSS-000.000.000.000
Example F1234567890-20000422105544-194.94.44.210
5. BioImage-DOI-to-Kernel Maps
5.1 The general BioImage DOI Genre (according to the first view)
|Kernel |BioImage DOI |
|(grey elements are the original kernel elements; white elements are extensions introduced by CrossRef) |(grey elements are BioImage-specific new elements) |
|Element/Definition |Status/ |Value |Comment |Element/Definition |Status/ |Value |Comment |
| |Number | | | |Number | | |
| | | | |head |Mandatory | | |
| | | | |XML-tag |1 only | | |
|Metadata Record Version |Mandatory |Number | |.doi_batch_id |Mandatory |String | |
|The version number of the |1 only | | |Batch file identifier |1 only | | |
|metadata | | | | | | | |
|Date of Metadata Declaration |Mandatory |YYYYMMDD | |.doi_batch_timestamp |Mandatory |YYYYMMDDHHMMSS | |
|The date on which this |1 only | | |Date and time the file was |1 only | | |
|declaration was made | | | |created | | | |
|Metadata Registrant |Mandatory | |A Registration Agency |.depositor |Mandatory | |Administrative Registration |
|The identity of the person or |1 only | | |The Registration Agency that |1 only | |Agency metadata |
|organization registering the DOI | | | |sends the information | | | |
| | | | |..depositor_id |Mandatory |DOI Prefix |Fixed for BioImage: BioImage |
| | | | |Registration Agency identifier |1 only | |DOI Prefix |
| | | | |..depositor_name |Optional |String | |
| | | | |The name of the person who sends |1 only | | |
| | | | |the information | | | |
| | | | |..email_address |Mandatory |Email |The email address may be |
| | | | |The email address of the person |1 only | |generic. For BioImage: |
| | | | |who sends the information | | |RA@ |
|Primary Agent |Mandatory |ID or Name from an |The specification of Primary |.registrant |Mandatory | |Administrative owner metadata|
|The name or identifier of the |All |agreed Genre namespace |Agent (normally but not |The owner of the information |All (1 minimum) | | |
|primary agent(s) | | |necessarily the creator) is | | | | |
| | | |determined in the extension | | | | |
| | | |rules for each DOI Genre. | | | | |
| | | | |..registrant_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The owner's name |1 only | | |
| | | | |..registrant_id |Qualified |Identifier |Optional as long as there is |
| | | | |The owner's identifier |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |...registrant_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
|Agent Role |Mandatory |Role from an agreed | |..registrant role |Mandatory |String |Fixed for BioImage: Database |
|The role(s) played by the primary|1 minimum |Genre namespace | |The role(s) played by the |1 minimum | |Provider? |
|agent(s) | | | |registrant (owner)? | | | |
| | | | |body |Mandatory | | |
| | | | |XML-tag |1 only | | |
| | | | |.doi_record |Mandatory | |All records have to belong to|
| | | | | |1 minimum | |the same owner (specified in |
| | | | | | | |the header) |
|Origination |Mandatory |{Original, Derivation, | |..doi_record type |Mandatory |{Original, |Study: original, derivation |
|The process by which the resource|1 minimum |Excerpt, Compilation, | |The process by which the resource|1 only |Derivation, |(citation), excerpt |
|is made | |Replica} | |is made | |Excerpt} |(abstract) |
| | | | | | | |File: original, derivation |
| | | | | | | |(thumbnail), excerpt (only |
| | | | | | | |image) |
| | | | |..doi_reference |Optional |DOI | |
| | | | |A reference to a related object |1 minimum | | |
| | | | |...doi_reference type |Mandatory |{Original, |Study: original, derivation |
| | | | |The type of the related object |1 only |Derivation, |(citation), excerpt |
| | | | |(doi_record type) | |Excerpt} |(abstract) |
| | | | | | | |File: original, derivation |
| | | | | | | |(thumbnail), excerpt (only |
| | | | | | | |image) |
| | | | |..doi_timestamp |Optional |YYYYMMDDHHMMSS | |
| | | | |Date and time the DOI record was |1 only | | |
| | | | |created | | | |
| | | | |..doi_data |Mandatory | | |
| | | | | |1 only | | |
|DOI |Mandatory |DOI |This is the key for this |...doi |Mandatory |DOI |This is the DOI for this |
|A DOI |1 only | |record |The DOI of the object (resource) |1 only | |record |
|URL resolution |Mandatory |URL | |...url |Mandatory |URL |1 minimum for multiple |
| |1 only | | |The URL(s) of the object |1 only | |resolution |
| | | | |(resource) | | | |
|DOI Genre |Mandatory |From DOI Genre tables | |..object_metadata |Mandatory | | |
|A class of resources with common |1 minimum | | | |1 only | | |
|characteristics defined by the | | | | | | | |
|IDF community | | | | | | | |
| | | | |...object |Mandatory | | |
| | | | |The object (resource) |1 only | | |
|Type |Mandatory |{Work, Physical | |....object type |Mandatory |{…} |For BioImage: {Study, |
|The primary structural type of |1 only |Manifestation, Digital | |The type of the resource |1 only | |Dataset, File} |
|the resource | |Manifestation, | | | | | |
| | |Performance} | | | | | |
| | | | |....object format |Optional |{…} |For BioImage files: {raw, |
| | | | |The format of the resource |1 only | |tiff, other}. |
| | | | | | | |Not applicable for BioImage |
| | | | | | | |studies and datasets |
|Title |Qualified |alphanumeric string |Mandatory unless the DOI |....title |Optional |string |For BioImage: Does not exist |
|A name by which the resource is |1 minimum | |Genre extension rules |The title of the resource |1 only | |currently for files |
|known | | |specifically exclude it | | | | |
| | | | |....author |Mandatory | |For compliance with CrossRef |
| | | | |The author(s) |1 minimum | | |
| | | | |.....author type |Mandatory |{first, additional, |Has to be revised for files |
| | | | |The author's role |1 only |corresponding} | |
| | | | |.....given_name |Optional |string | |
| | | | |The author’s first name |1 only | | |
| | | | |.....surname |Mandatory |string | |
| | | | |The author’s last name |1 only | | |
| | | | |....copyright_holder |Optional | |This can be a person or an |
| | | | |The copyright holder (owner) of |1 only | |institution (for BioImage |
| | | | |the resource | | |studies and datasets it's |
| | | | | | | |BioImage) |
| | | | |.....crh_name |Mandatory |String | |
| | | | |The copyright holder's name |1 only | | |
| | | | |.....crh_id |Qualified |Identifier |Optional as long as there is |
| | | | |The copyright holder's identifier|1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |......crh_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
| | | | |....date |Mandatory | |For compliance with CrossRef.|
| | | | |A date for the resource |1 minimum | |No date types currenly |
| | | | | | | |implemented in BioImage |
| | | | |.....date type |Optional |{…} | |
| | | | |The date type (e.g. submission |1 only | | |
| | | | |date) | | | |
| | | | |.....year |Mandatory |YYYY |May be replaced by timestamp |
| | | | | |1 only | | |
| | | | |.....month |Optional |MM | |
| | | | | |1 only | | |
| | | | |.....day |Optional |DD | |
| | | | | |1 only | | |
| | | | |....enumeration |Mandatory | |For compliance with CrossRef.|
| | | | | |1 only | |Citation format for BioImage:|
| | | | | | | |N.N. Author, BioImage StudyID|
| | | | | | | |(DatasetID), FileID (Year). |
| | | | | | | |The year still has to be |
| | | | | | | |specified. |
| | | | |.....top_level |Mandatory |Identifier |Corresponds to journal |
| | | | |The top-level parent in the |1 only | |volume. For BioImage: StudyID|
| | | | |hierarchy | | | |
| | | | |.....second_level |Optional |Identifier |Corresponds to journal issue.|
| | | | |An intermediate parent in the |1 only | |For BioImage: DatasetID |
| | | | |hierarchy | | | |
|Identifier |Qualified |ID-string |Mandatory unless the DOI |....identifier |Mandatory |Identifier |For BioImage: BioImageID |
|A unique identifier (e.g. from a |1 minimum | |Genre extension rules |The identifier of the resource |1 minimum | | |
|legacy scheme) applied to the | | |specifically exclude it | | | | |
|resources | | | | | | | |
| | | | |.....identifier type |Mandatory |{BioImageID, DOI, | |
| | | | |The type of the identifier |1 only |other} | |
| | | | |...database |Mandatory | |This is the database, not the|
| | | | |The database that stores the |1 only | |database provider (the |
| | | | |object | | |registrant) |
| | | | |....database_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The name of the database |1 only | | |
| | | | |....database_id |Qualified |Identifier |Optional as long as there is |
| | | | |The identifier of the database |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |.....database_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
5.2 Comments
This model tries to stick as closely as possible to the structure and terminology introduced by CrossRef for the DOI-X. However, this leads to some conflicts, especially regarding the following points:
• Registrant, depositor, copyright holder
It is unfortunate that CrossRef introduced a registrant (the information provider) that is not identical to the DOI kernel registrant (the Registration Agency) defined by IDF. The Registration Agency is named depositor by CrossRef. The registrant in the CrossRef model is the primary agent in the DOI kernel. While using registrant and depositor in the CrossRef sense, I introduced a copyright holder. This is not the registrant in the CrossRef sense (actually, the registrant is the metadata owner, not the resource owner).
So we have:
|Kernel |CrossRef |BioImage |Definition |
|primary agent |registrant |registrant |information (=metadata) and resource provider; |
| | | |metadata owner, not always resource owner |
|registrant |depositor |depositor |Registration Agency that submits the metadata |
|- |- |copyright holder |resource owner |
The nomenclature should be revised in accordance with the indecs terminology.
• Metadata Record Version, Date of Metadata Declaration
CrossRef introduced two new elements: Metadata Record Version (MRV) and Date of Metadata Declaration (DMD). Although they say that the MRV identifies the version of the metadata, they map it to the doi_batch_id, which is not able to identify a version number. The version number in DOI-X is given by the timestamp. However, the timestamp is only mapped to the DMD. Although I use the same structure, it seems better to map the MRV and the DMD to a timestamp. To be strict, one would have to introduce a Metadata Record ID in the DOI kernel that corresponds to the doi_batch_id. This raises the question whether there should be a doi_record_id to identify the individual records in the batch file. It suggests that all kernel elements should be mapped to doi records rather than to the batch file.
• Primary Agent (in the kernel; here registrant)
One thing that is not completely clear is the primary agent (kernel element). Why can there be more than one? CrossRef restricts the number to one, and this is the only way to put it into the file header (such that it is globally valid).
• Object_metadata and object
The object_metadata tag encloses an object tag (and a database tag). This seems to deepen the hierarchy too much. Both tags can be unified (and the database tag could either be in it or at the same level).
• Given_name and surname; year, month and day
The given_name and the surname could be merged as well. The same is valid for year, month and day, which could be replaced by a timestamp.
• Enumeration
As discussed elsewhere the enumeration tag, which provides the hierarchy that is necessary for bibliographic citations, is not necessary for databases in which all elements are uniquely identified by an id. Therefore the tag could be dropped or made optional.
5.3 DOI-E-to-Kernel Map
This DOI-Genre reflects the third view. It applies to the BioImage entities study and dataset. Files are described by a DOI-I (see next section).
|Kernel |DOI-I |
|(grey elements are the original kernel elements; white elements are extensions introduced by CrossRef) |(grey elements are BioImage-specific new elements) |
|Element/Definition |Status/ |Value |Comment |Element/Definition |Status/ |Value |Comment |
| |Number | | | |Number | | |
| | | | |head |Mandatory | | |
| | | | |XML-tag |1 only | | |
|Metadata Record Version |Mandatory |Number | |.doi_batch_id |Mandatory |String | |
|The version number of the |1 only | | |Batch file identifier |1 only | | |
|metadata | | | | | | | |
|Date of Metadata Declaration |Mandatory |YYYYMMDD | |.doi_batch_timestamp |Mandatory |YYYYMMDDHHMMSS | |
|The date on which this |1 only | | |Date and time the file was |1 only | | |
|declaration was made | | | |created | | | |
|Metadata Registrant |Mandatory | |A Registration Agency |.depositor |Mandatory | |Administrative Registration |
|The identity of the person or |1 only | | |The Registration Agency that |1 only | |Agency metadata |
|organization registering the DOI | | | |sends the information | | | |
| | | | |..depositor_id |Mandatory |DOI Prefix |Fixed for BioImage: BioImage |
| | | | |Registration Agency identifier |1 only | |DOI Prefix |
| | | | |..depositor_name |Optional |String | |
| | | | |The name of the person who sends |1 only | | |
| | | | |the information | | | |
| | | | |..email_address |Mandatory |Email |The email address may be |
| | | | |The email address of the person |1 only | |generic. For BioImage: |
| | | | |who sends the information | | |RA@ |
|Primary Agent |Mandatory |ID or Name from an |The specification of Primary |.registrant |Mandatory | |Administrative owner metadata|
|The name or identifier of the |All |agreed Genre namespace |Agent (normally but not |The owner of the information |All (1 minimum) | | |
|primary agent(s) | | |necessarily the creator) is | | | | |
| | | |determined in the extension | | | | |
| | | |rules for each DOI Genre. | | | | |
| | | | |..registrant_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The owner's name |1 only | | |
| | | | |..registrant_id |Qualified |Identifier |Optional as long as there is |
| | | | |The owner's identifier |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |...registrant_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
|Agent Role |Mandatory |Role from an agreed | |..registrant role |Mandatory |String |Fixed for BioImage: Database |
|The role(s) played by the primary|1 minimum |Genre namespace | |The role(s) played by the |1 minimum | |Provider? |
|agent(s) | | | |registrant (owner)? | | | |
| | | | |body |Mandatory | | |
| | | | |XML-tag |1 only | | |
| | | | |.doi_record |Mandatory | |All records have to belong to|
| | | | | |1 minimum | |the same owner (specified in |
| | | | | | | |the header) |
|Origination |Mandatory |{Original, Derivation, | |..doi_record type |Mandatory |{Original, |Study: original, derivation |
|The process by which the resource|1 minimum |Excerpt, Compilation, | |The process by which the resource|1 only |Derivation, |(citation), excerpt |
|is made | |Replica} | |is made | |Excerpt} |(abstract) |
| | | | |..doi_reference |Optional |DOI | |
| | | | |A reference to a related object |1 minimum | | |
| | | | |...doi_reference type |Mandatory |{Original, |Study: original, derivation |
| | | | |The type of the related object |1 only |Derivation, |(citation), excerpt |
| | | | |(doi_record type) | |Excerpt} |(abstract) |
| | | | |..doi_timestamp |Optional |YYYYMMDDHHMMSS | |
| | | | |Date and time the DOI record was |1 only | | |
| | | | |created | | | |
| | | | |..doi_data |Mandatory | | |
| | | | | |1 only | | |
|DOI |Mandatory |DOI |This is the key for this |...doi |Mandatory |DOI |This is the DOI for this |
|A DOI |1 only | |record |The DOI of the object (resource) |1 only | |record |
|URL resolution |Mandatory |URL | |...url |Mandatory |URL |1 minimum for multiple |
| |1 only | | |The URL(s) of the object |1 only | |resolution |
| | | | |(resource) | | | |
|DOI Genre |Mandatory |From DOI Genre tables | |..object_metadata |Mandatory | | |
|A class of resources with common |1 minimum | | | |1 only | | |
|characteristics defined by the | | | | | | | |
|IDF community | | | | | | | |
| | | | |...object |Mandatory | | |
| | | | |The object (resource) |1 only | | |
|Type |Mandatory |{Work, Physical | |....object type |Mandatory |{…} |For BioImage: {Study, |
|The primary structural type of |1 only |Manifestation, Digital | |The type of the resource |1 only | |Dataset} |
|the resource | |Manifestation, | | | | | |
| | |Performance} | | | | | |
|Title |Qualified |alphanumeric string |Mandatory unless the DOI |....title |Optional |string | |
|A name by which the resource is |1 minimum | |Genre extension rules |The title of the resource |1 only | | |
|known | | |specifically exclude it | | | | |
| | | | |....author |Mandatory |string |For compliance with CrossRef |
| | | | |The author(s)´s name |1 minimum | | |
| | | | |.....author type |Mandatory |{first, additional, | |
| | | | |The author's role |1 only |corresponding} | |
| | | | |....copyright_holder |Optional | |For BioImage studies and |
| | | | |The copyright holder (owner) of |1 only | |datasets it's BioImage |
| | | | |the resource | | | |
| | | | |.....crh_name |Mandatory |String | |
| | | | |The copyright holder's name |1 only | | |
| | | | |.....crh_id |Qualified |Identifier |Optional as long as there is |
| | | | |The copyright holder's identifier|1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |......crh_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
| | | | |....date |Mandatory |YYYYMMDDHHMMSS |For compliance with CrossRef.|
| | | | |A date for the resource |1 minimum | |No date types currenly |
| | | | | | | |implemented in BioImage |
| | | | |.....date type |Optional |{…} | |
| | | | |The date type (e.g. submission |1 only | | |
| | | | |date) | | | |
| | | | |....enumeration |Mandatory | |For compliance with CrossRef.|
| | | | | |1 only | |Citation format for BioImage:|
| | | | | | | |N.N. Author, BioImage StudyID|
| | | | | | | |(DatasetID), FileID (Year). |
| | | | | | | |The year still has to be |
| | | | | | | |specified. |
| | | | |.....top_level |Mandatory |Identifier |Corresponds to journal |
| | | | |The top-level parent in the |1 only | |volume. For BioImage: StudyID|
| | | | |hierarchy | | | |
| | | | |.....second_level |Optional |Identifier |Corresponds to journal issue.|
| | | | |An intermediate parent in the |1 only | |For BioImage: DatasetID |
| | | | |hierarchy | | | |
|Identifier |Qualified |ID-string |Mandatory unless the DOI |....identifier |Mandatory |Identifier |For BioImage: BioImageID |
|A unique identifier (e.g. from a |1 minimum | |Genre extension rules |The identifier of the resource |1 minimum | | |
|legacy scheme) applied to the | | |specifically exclude it | | | | |
|resources | | | | | | | |
| | | | |.....identifier type |Mandatory |{BioImageID, DOI, | |
| | | | |The type of the identifier |1 only |other} | |
| | | | |...database |Mandatory | |This is the database, not the|
| | | | |The database that stores the |1 only | |database provider (the |
| | | | |object | | |registrant) |
| | | | |....database_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The name of the database |1 only | | |
| | | | |....database_id |Qualified |Identifier |Optional as long as there is |
| | | | |The identifier of the database |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |.....database_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
5.4 DOI-I-to-Kernel Map
This DOI Genre reflects the third view. It is for images only (images, figures, data files). BioImage studies and datasets belong to the DOI-E Genre
|Kernel |DOI-I |
|(grey elements are the original kernel elements; white elements are extensions introduced by CrossRef) |(grey elements are BioImage-specific new elements) |
|Element/Definition |Status/ |Value |Comment |Element/Definition |Status/ |Value |Comment |
| |Number | | | |Number | | |
| | | | |head |Mandatory | | |
| | | | |XML-tag |1 only | | |
|Metadata Record Version |Mandatory |Number | |.doi_batch_id |Mandatory |String | |
|The version number of the |1 only | | |Batch file identifier |1 only | | |
|metadata | | | | | | | |
|Date of Metadata Declaration |Mandatory |YYYYMMDD | |.doi_batch_timestamp |Mandatory |YYYYMMDDHHMMSS | |
|The date on which this |1 only | | |Date and time the file was |1 only | | |
|declaration was made | | | |created | | | |
|Metadata Registrant |Mandatory | |A Registration Agency |.depositor |Mandatory | |Administrative Registration |
|The identity of the person or |1 only | | |The Registration Agency that |1 only | |Agency metadata |
|organization registering the DOI | | | |sends the information | | | |
| | | | |..depositor_id |Mandatory |DOI Prefix |Fixed for BioImage: BioImage |
| | | | |Registration Agency identifier |1 only | |DOI Prefix |
| | | | |..depositor_name |Optional |String | |
| | | | |The name of the person who sends |1 only | | |
| | | | |the information | | | |
| | | | |..email_address |Mandatory |Email |The email address may be |
| | | | |The email address of the person |1 only | |generic. For BioImage: |
| | | | |who sends the information | | |RA@ |
|Primary Agent |Mandatory |ID or Name from an |The specification of Primary |.registrant |Mandatory | |Administrative owner metadata|
|The name or identifier of the |All |agreed Genre namespace |Agent (normally but not |The owner of the information |All (1 minimum) | | |
|primary agent(s) | | |necessarily the creator) is | | | | |
| | | |determined in the extension | | | | |
| | | |rules for each DOI Genre. | | | | |
| | | | |..registrant_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The owner's name |1 only | | |
| | | | |..registrant_id |Qualified |Identifier |Optional as long as there is |
| | | | |The owner's identifier |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |...registrant_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
|Agent Role |Mandatory |Role from an agreed | |..registrant role |Mandatory |String |Fixed for BioImage: Database |
|The role(s) played by the primary|1 minimum |Genre namespace | |The role(s) played by the |1 minimum | |Provider? |
|agent(s) | | | |registrant (owner)? | | | |
| | | | |body |Mandatory | | |
| | | | |XML-tag |1 only | | |
| | | | |.doi_record |Mandatory | |All records have to belong to|
| | | | | |1 minimum | |the same owner (specified in |
| | | | | | | |the header) |
|Origination |Mandatory |{Original, Derivation, | |..doi_record type |Mandatory |{Original, |File: original (generic |
|The process by which the resource|1 minimum |Excerpt, Compilation, | |The process by which the resource|1 only |Derivation, |data), derivation (image), |
|is made | |Replica} | |is made | |Excerpt, Compilation} |excerpt (partial image), |
| | | | | | | |compilation (composite |
| | | | | | | |figure) |
| | | | |..doi_reference |Optional |DOI |The related object can be |
| | | | |A reference to a related object |1 minimum | |e.g. the original source |
| | | | | | | |(generic data) |
| | | | |...doi_reference type |Mandatory |{Original, |File: original (generic |
| | | | |The type of the related object |1 only |Derivation, |data), derivation (image), |
| | | | |(doi_record type) | |Excerpt, Compilation} |excerpt (partial image), |
| | | | | | | |compilation (composite |
| | | | | | | |figure) |
| | | | |..doi_timestamp |Optional |YYYYMMDDHHMMSS | |
| | | | |Date and time the DOI record was |1 only | | |
| | | | |created | | | |
| | | | |..doi_data |Mandatory | | |
| | | | | |1 only | | |
|DOI |Mandatory |DOI |This is the key for this |...doi |Mandatory |DOI |This is the DOI for this |
|A DOI |1 only | |record |The DOI of the object (resource) |1 only | |record |
|URL resolution |Mandatory |URL | |...url |Mandatory |URL |1 minimum for multiple |
| |1 only | | |The URL(s) of the object |1 only | |resolution |
| | | | |(resource) | | | |
|DOI Genre |Mandatory |From DOI Genre tables | |..object_metadata |Mandatory | | |
|A class of resources with common |1 minimum | | | |1 only | | |
|characteristics defined by the | | | | | | | |
|IDF community | | | | | | | |
| | | | |...object |Mandatory | | |
| | | | |The object (resource) |1 only | | |
|Type |Mandatory |{Work, Physical | |....object type |Mandatory |{…} |For BioImage: {Video, 3D Data|
|The primary structural type of |1 only |Manifestation, Digital | |The type of the resource |1 only | |Set, other} |
|the resource | |Manifestation, | | | | | |
| | |Performance} | | | | | |
| | | | |....object format |Optional |{…} |For BioImage files: {raw, |
| | | | |The format of the resource |1 only | |tiff, other}. |
| | | | |....size |Optional |number |Criterion for integrity check|
| | | | |The size of the resource (in |1 only | | |
| | | | |Kbytes or Mbytes) | | | |
| | | | |....compression |Optional |{…, other, none} |May be relevant for |
| | | | |The compression algorithm applied|1 only | |functional granularity issues|
| | | | |to the file | | | |
| | | | |....resolution |Optional |set of numbers |May be relevant for |
| | | | |The number of pixels per axis |1 only | |functional granularity |
| | | | |(for all axes, including time) | | |issues. 0 for non-digital |
| | | | | | | |images |
| | | | |....quality |Optional |number |May be relevant for |
| | | | |The dynamic range of the data (in|1 only | |functional granularity |
| | | | |bits per pixel) | | |issues. 0 for non-digital |
| | | | | | | |images |
|Title |Qualified |alphanumeric string |Mandatory unless the DOI |....title |Optional |string |Does not exist currently for |
|A name by which the resource is |1 minimum | |Genre extension rules |The title of the resource |1 only | |BioImage files (only for |
|known | | |specifically exclude it | | | |videos) |
| | | | |....subject |Optional |string |Keyword related to subject |
| | | | |The subject or content of the |1 minimum | |(Art, Biology, etc.) or |
| | | | |resource | | |content (Napoleon, zebrafish,|
| | | | | | | |etc.) |
| | | | |....author |Mandatory |string |For compliance with CrossRef.|
| | | | |The author(s)´s name |1 minimum | |Does not exist currently for |
| | | | | | | |BioImage files |
| | | | |.....author type |Mandatory |{first, additional, |Has to be revised for files |
| | | | |The author(s)'s role |1 only |corresponding} | |
| | | | |....copyright_holder |Optional | |This can be a person or an |
| | | | |The copyright holder (owner) of |1 only | |institution |
| | | | |the resource | | | |
| | | | |.....crh_name |Mandatory |string | |
| | | | |The copyright holder's name |1 only | | |
| | | | |.....crh_id |Qualified |identifier |Optional as long as there is |
| | | | |The copyright holder's identifier|1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |......crh_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
| | | | |....date |Mandatory |YYYYMMDDHHMMSS |For compliance with CrossRef.|
| | | | |A date for the resource |1 minimum | |No date types currenly |
| | | | |(timestamp) | | |implemented in BioImage |
| | | | |.....date type |Optional |{…} | |
| | | | |The date type (e.g. submission |1 only | | |
| | | | |date) | | | |
|Identifier |Qualified |ID-string |Mandatory unless the DOI |....identifier |Mandatory |Identifier |For BioImage: BioImageID |
|A unique identifier (e.g. from a |1 minimum | |Genre extension rules |The identifier of the resource |1 minimum | | |
|legacy scheme) applied to the | | |specifically exclude it | | | | |
|resources | | | | | | | |
| | | | |.....identifier type |Mandatory |{BioImageID, DOI, | |
| | | | |The type of the identifier |1 only |other} | |
| | | | |...database |Mandatory | |This is the database, not the|
| | | | |The database that stores the |1 only | |database provider (the |
| | | | |object | | |registrant) |
| | | | |....database_name |Mandatory |String |Fixed for BioImage: BioImage |
| | | | |The name of the database |1 only | | |
| | | | |....database_id |Qualified |Identifier |Optional as long as there is |
| | | | |The identifier of the database |1 only | |no identification system for |
| | | | | | | |databases. Mandatory if there|
| | | | | | | |is such as system |
| | | | |.....database_id type |Qualified |{…} | |
| | | | |The type of the identifier |1 only | | |
6. XML-DTDs for BioImage DOI Genres
6.1 XML-DTD for the general BioImage DOI Genre
This part describes a Document Type Definition for the BioImage database. It is based on the first view and the general BioImage DOI defined previously. The structure matches the CrossRef DOI-X Document Type Definition as closely as possible. A first version of this DTD was designed for ingenta in Jan./Feb. 2000.
|Document Type Definition |XML Document Example |
| |(italics mark information that does not yet exist) |
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| |123456 |
| |19990628123304 |
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| |10.9999 |
| |Bob Smith |
| |smith@ |
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| |BioImage |
| |999 |
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| |10.9999/F007-0 |
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| |19990628123304 |
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| |Paul |
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| |John Johnson |
| |999 |
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| |1999 |
| |11 |
| |19 |
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| |BioImage |
| |999 |
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This requires some changes in the current BioImage database model. For instance, a timestamp has to be introduced for the DOI. This can be handled with a DOI table:
DOI (doi, url, timestamp, record_type).
It also requires a date for the study (currently available in the audit table).
6.2 XML-DTDs for DOI-I and DOI-E
This part describes a Document Type Definition for DOI-I and DOI-E. It is based on the third view and the DOI Genres defined previously. DOI-I is for images, figures, and data files. DOI-E is for electronic publications such as the BioImage study and dataset.
|Document Type Definition DOI-I |Document Type Definition DOI-E |
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