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acta_annotated_to_modern_bib.json
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The following object is closer to bibjson than the original acta example.
There are comments at the top here, and also within the JSON, so this doc is not valid JSON, but is an example.
The whole lot was taken out of the wrapping JSON object and the containing "recordList" - a bibjson object can stand alone
and only needs to be wrapped in a "records" list if it is being provided as part of a wrapping collection object
The pmc ID had to be moved into a new identifer list.
The pmid had to be moved into the identifier list.
The title had the newlines stripped from it
The ID was removed it is not particularly needed in itself, although it can be set if desired.
The x-... ones at the top appear to be internally specified, are not previously part of bibjson.
However would it be worth considering specifying a "source" key in bibjson where data about the source of the record is stored?
{
"x-fabio-type": "Expression", # these x- types are not used in bibjson but can be kept without causing issue
"x-in-text-reference-pointer-count": "28",
"x-reference-count": "22",
"x-source-type": "pmc_oa",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
# We need a wee bit of metadata to keep bibserver happy
"_id": "...", # this can either be provided at upload or it will be created for you (as described, you can call the make_id function from bibserver code if necessary
"_collection": ["opencitations"],
"_created_by": <someusername>,
"_created": datetime.now().strftime("%Y-%m-%d %H%M")
This group here are standard bibjson now
"type": "Article",
"title": "Range of motion exercise of temporo-mandibular joint with hot pack increases occlusal force in patients with Duchenne muscular dystrophy",
"identifier": [
{
"type": "pmc",
"id": "3146337"
},
{
"type": "pmid",
"id": "21574523"
}
],
"abstract": "The purpose of this study is to evaluate whether the range of motion exercise of the temporo-mandibular joint (jaw ROM exercise) with a hot pack and massage of the masseter muscle improve biting disorder in Duchenne muscular dystrophy (DMD). The subjects were 18 DMD patients (21.3 \u00b1 4.1 years old). The jaw ROM exercise consisted of therapist-assisted training (2 times a week) and self-training (before each meal every day). The therapist-assisted training consisted of the application of a hot pack on the cheek of the masseter muscle region (15 minutes), the massage of the masseter (10 minutes), and jaw ROM exercise (5 minutes). The self-training involved jaw ROM exercise by opening the mouth to the maximum degree, ten times. These trainings continued for six months. Outcomes were evaluated by measuring the greatest occlusal force and the distance at the maximum degree of mouth opening between an incisor of the top and that of the bottom. Six months later, the greatest occlusal force had increased significantly compared with that at the start of jaw ROM exercise (intermediate values: from 73.8N to 97.3N) (p = 0.005) as determined by the Friedman test and Scheff\u00e9's nonparametric test. The patients' satisfaction with meals increased. However, the maximum degree of mouth opening did not change after six months of jaw ROM exercise. Jaw ROM exercise in DMD is effective for increasing the greatest occlusal force.",
"volume": "29",
"year": "2010",
"month": "12",
"pages": "392--397",
"pageStart": "392", # these are not common in bibjson, usually just pages string is used. But these do not need to be removed
"pageEnd": "397",
whilst bibjson does state you can use the rules of JSON-LD to reference other objects, there is little value for doing that within
our index. So the journal object should be contained within the record object as below, rather than a ref item
NOTE ALSO the journal should have a "name", and this one does not appear to have one. If there is no known name, perhaps the
x-nlm-ta should be used as the name too.
"journal": {
"publisher": {
"id": "pmid:21574523:publisher",
"name": "Pacini Editore SpA"
},
"identifier":[
{
"type": "issn",
"id": "1128-2460"
},
{
"eissn": "1128-2460"
],
"x-nlm-ta": "Acta Myol",
},
Similarly, these author objects should just be internal to the record object unless we do decide to go with separated author entities.
I have not written them all in below, but essentially each of these author objects that contains a "ref" should actually just contain
the author data directly. Look at the author list below to see an example of the content of an author object
"author": [
{
"ref": "@pmid:21574523:contributor:1"
},
{
"ref": "@pmid:21574523:contributor:2"
},
{
"ref": "@pmid:21574523:contributor:3"
},
{
"ref": "@pmid:21574523:contributor:4"
},
{
"ref": "@pmid:21574523:contributor:5"
},
{
"ref": "@pmid:21574523:contributor:6"
},
{
"ref": "@pmid:21574523:contributor:7"
}
],
The "cites" object has been changed in name to "citation" to better fit modern bibjson approach
Now, because citation objects are full record objects, and because we care about citations in this project,
there is value in the citations being full record objects.
So, when a record is supplied to our index from the pipeline, it should contain a citation list that is just a list of
objects with "ref" but "ref" must point to the _id of that record object in our index. If it does not yet exist in our
index, then create the record object then add its _id to the citation list.
Here we can also consider nesting on the index if necessary, although it is not an immediate requirement.
"citation": [
{
"ref": "@pmid:21574523:reference:R01"
},
{
"ref": "@pmid:21574523:reference:R02"
},
{
"ref": "@pmid:21574523:reference:R03"
},
{
"ref": "@pmid:21574523:reference:R04"
},
{
"ref": "@pmid:21574523:reference:R05"
},
{
"ref": "@pmid:21574523:reference:R06"
},
{
"ref": "@pmid:21574523:reference:R07"
},
{
"ref": "@pmid:21574523:reference:R08"
},
{
"ref": "@pmid:21574523:reference:R09"
},
{
"ref": "@pmid:21574523:reference:R10"
},
{
"ref": "@pmid:21574523:reference:R11"
},
{
"ref": "@pmid:21574523:reference:R12"
},
{
"ref": "@pmid:21574523:reference:R13"
},
{
"ref": "@pmid:21574523:reference:R14"
},
{
"ref": "@pmid:21574523:reference:R15"
},
{
"ref": "@pmid:21574523:reference:R16"
},
{
"ref": "@pmid:21574523:reference:R17"
},
{
"ref": "@pmid:21574523:reference:R18"
},
{
"ref": "@pmid:21574523:reference:R19"
},
{
"ref": "@pmid:21574523:reference:R20"
},
{
"ref": "@pmid:21574523:reference:R21"
},
{
"ref": "@pmid:21574523:reference:R22"
}
]
}
# the useful parts of the journal item here were pulled into the bibjson object above
{
"publisher": {
"ref": "@pmid:21574523:publisher"
},
"issn": "1128-2460",
"x-nlm-ta": "Acta Myol",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"eissn": "1128-2460",
"type": "Journal",
"id": "pmid:21574523:journal"
},
# and this publisher object was pulled into the above journal object
{
"type": "Organization",
"id": "pmid:21574523:publisher",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"name": "Pacini Editore SpA"
},
# these author objects should be internal to the record object. The first author object is altered here to fit bibjson
# this is the altered first author
# x-surname changed to lastname
# x-source-url, x-given-names, x-name-style removed. Could be left in if desired, but not obviously useful
# id removed
# type removed - it is inherent
# the affiliation data has been wrapped into this author object too - name was stripped from address, if possible.
Otherwise just make the name the same as the address
Also remove the ; from the end of the address string
{
"name": "Nozaki, S.",
"lastname": "Nozaki",
"affiliation": {
"name": "Hyogo University of Health Science",
"address": " Hyogo University of Health Science, School of Rehabilitation, Japan"
}
}
# here is the original author list
{
"x-surname": "Nozaki",
"name": "Nozaki, S.",
"x-given-names": "S.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A1"
},
"type": "Person",
"id": "pmid:21574523:contributor:1"
},
{
"x-surname": "Kawai",
"name": "Kawai, M.",
"x-given-names": "M.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A2"
},
"type": "Person",
"id": "pmid:21574523:contributor:2"
},
{
"x-surname": "Shimoyama",
"name": "Shimoyama, R.",
"x-given-names": "R.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A3"
},
"type": "Person",
"id": "pmid:21574523:contributor:3"
},
{
"x-surname": "Futamura",
"name": "Futamura, N.",
"x-given-names": "N.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A4"
},
"type": "Person",
"id": "pmid:21574523:contributor:4"
},
{
"x-surname": "Matsumura",
"name": "Matsumura, T.",
"x-given-names": "T.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A5"
},
"type": "Person",
"id": "pmid:21574523:contributor:5"
},
{
"x-surname": "Adachi",
"name": "Adachi, K.",
"x-given-names": "K.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A6"
},
"type": "Person",
"id": "pmid:21574523:contributor:6"
},
{
"x-surname": "Kikuchi",
"name": "Kikuchi, Y.",
"x-given-names": "Y.",
"x-name-style": "western",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"affiliated": {
"ref": "@pmid:21574523:affiliation:A7"
},
"type": "Person",
"id": "pmid:21574523:contributor:7"
},
# here are the organisations
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A1",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Hyogo University of Health Science, School of Rehabilitation, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A2",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Higashisaitama National Hospital, Department of Neurology, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A3",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Matsue Medical Center, Department of Neurology, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A4",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Hyogochuo National Hospital, Department of Neurology, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A5",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Toneyama National Hospital, Department of Neurology, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A6",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Tokushima National Hospital, Department of Neurology, Japan;"
},
{
"type": "Organization",
"id": "pmid:21574523:affiliation:A7",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"address": " Nagasaki University Graduate School of Biomedical Science, Japan"
},
# here are the citations and then their authors and so on
{
"x-fabio-type": "JournalArticle",
"citation": "Botteron S Verdebout CM Jeannet PY Orofacial dysfunction in Duchenne muscular dystrophy Arch Oral Biol 2009 54 26 31 18805518",
"author": [
{
"ref": "@pmid:21574523:reference:R01:contributor:1"
},
{
"ref": "@pmid:21574523:reference:R01:contributor:2"
},
{
"ref": "@pmid:21574523:reference:R01:contributor:3"
}
],
"journal": {
"ref": "@pmid:21574523:reference:R01:journal"
},
"title": "Orofacial dysfunction\nin Duchenne muscular dystrophy",
"pageStart": "26",
"volume": "54",
"x-source-type": "pmc_oa_reference",
"pages": "26--31",
"x-source-url": "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/96/f2/Acta_Myol_2010_Dec_29(3)_392-397.tar.gz",
"year": "2009",
"pmid": "18805518",
"pageEnd": "31",
"type": "Article",
"id": "pmid:21574523:reference:R01"
},
{
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