How should we map publication types?

[NoisyFlowers]

PBot list of publication types:

• journal article
• standalone book
• edited book of contributed articles
• contributed article in edited book
• unpublished

(In addition, pbot has a bookType property. It is a string, not an enumeration. I'm not sure how we use it, but maybe for the other types in pbdb1s list that are obviously books?)

PBDB1 list of publication types:

• journal article
• Book
• book chapter
• book/book chapter
• serial monograph
• Compendium
• Ph.D. Thesis
• M.S. Thesis
• Abstract
• Guidebook
• news article
• Unpublished

How should be map these?

[NoisyFlowers]

PBot publication type notes

(based on our client form code)

Pbot Reference properties:

• reference
• title
• publicationType
• firstPage
• lastPage
• journal
• publicationVolume
• publicationNumber
• bookTitle
• publisher
• description
• bookType
• editors
• notes
• year
• authors
• doi
• pbdbid

journal article required properties

• year
• title
• journal
• publicationVolume
• authors
• pbdbid

standalone book required properties

• year
• title
• firstPage
• lastPage
• authors
• publisher
• bookType

edited book of contributed articles required properties

• year
• title
• firstPage
• lastPage
• editors
• publisher
• pbdbid

contributed article in edited book required properties

• year
• title
• firstPage
• lastPage
• authors
• editors
• publisher
• pbdbid

unpublished required properties

• year
• title
• description
• authors

Only required fields are enforced. No attempt is made to weed out meaningless fields per publication type.

[NoisyFlowers]

PBDB publication type notes

(based on our JSON Schema definitions for the upload API)

properties required for all publication types

• publication_type
• reftitle
• author1init
• author1last
• pubyr
• firstpage

properties optional for all publication types

• author2init
• author2last
• otherauthors
• lastpage
• doi
• language (enum: ['Chinese','English','French','German','Italian','Japanese','Portugese','Russian','Spanish','other','unknown'])
• comments
• classification_quality (enum: ['authoritative','standard','compendium'])
• basis (enum: ['','stated with evidence','stated without evidence','second hand','none discussed','not entered'])
• project_name (array of enum: ['decapod','ETE','5%','1%','PACED','PGAP','fossil record'])

journal article required properties

• pubtitle
• pubvol

journal article optional properties

• pubno

book, serial monograph, compendium, Ph.D. thesis, M.S. thesis, guidebook required properties

• publication_type
• publisher

book, serial monograph, compendium, Ph.D. thesis, M.S. thesis, guidebook optional properties

• pubcity

book chapter required properties

• pubtitle
• publisher
• editors

book chapter optional properties

• pubcity

book/book chapter required properties

• publisher
• editors

book/book chapter optional properties

• pubcity

[aazaff]

This is the kind of thing we need to push to the others ti weigh in on. As a temporary measure for your testing, maybe just pick one clearly mappable set and just filter out the rest. Journal article to Journal Article?

[NoisyFlowers]

I don't think we should have any duplicate publicationTypes (e.g. types that share identical required and optional fields).

Maybe something like this for mapping to pbdb2?

pbot

1. journal article
2. standalone book
3. contributed article in edited book
4. edited book of contributed articles --> edited volume or edited collection
5. unpublished

pbdb1

1. journal article
2. book, serial monograph, compendium, Ph.D. thesis, M.S. thesis, guidebook
3. book chapter
4. book/book chapter
5. unpublished

pbdb2

1. journal article
2. book (with bookType enum property for other pbdb1 values)
3. chapter
4. edited collection
5. unpublished (with documentType enum property similar to bookType. actually, could just have same property for both if the enum values are the same)

It might make sense to drop unpublished as a publicationType and just make it a required boolean property in the others that defaults to false.

[NoisyFlowers]

I've just created a SchemaDefinitions folder at the top of this repo. In it, we will keep the developing schemas as we flesh out the JSONB payloads of each entity table.

The first schema I've added there is for Reference. It's a tentative definition based on the previous comment.

[aazaff]

PBDB Abstract

Journal Article

{
"oid": "ref:38688",
"pty": "abstract",
"tit": "Shipworm pallets from the Paleocene (Cannonball Formation) of North Dakota",
"pby": "1965",
"ai1": "A. M.",
"al1": "Cvancara",
"pbt": "Geological Society of America Abstracts",
"vol": "1965",
"pgf": "38",
"pgl": "39",
"lan": "English"
}

Book

A problem for book we have noticed is that it is wildly inconsistent whether the book title is listed under "reftitle" or "pubtitle" in pbdb

{
"oid": "ref:86265",
"pty": "book",
"tit": "Systematic paleontology of the Lower Cretaceous deposits of Maryland: Mollusca",
"pby": "1911",
"ai1": "W. B.",
"al1": "Clark",
"eds": "W. B. Clark, A. B. Bibbins, E. W. Berry, & R. S. Lull",
"pbl": "Maryland Geological Survey",
"pbc": "Baltimore",
"pgf": "211",
"pgl": "213",
"lan": "English"
},
{
"oid": "ref:72824",
"pty": "book",
"pby": "1905",
"ai1": "P.",
"al1": "Choffat",
"pbt": "Contributions a la Connaissance Géologique des Colonies Portugaises d'Afrique. II. Nouvelles Données sur la Zone Littorale d'Angola",
"pbl": "Commision du Service Géologique du Portugal",
"pbc": "Lisbon",
"pgf": "1",
"pgl": "48",
"lan": "French"
}

Book/Book Title

Should go under "contributed article in edited book"

{
"oid": "ref:74603",
"pty": "book chapter",
"tit": "Bivalvia (Mollusca) of the Gulf of Mexico",
"pby": "2009",
"ai1": "D. D.",
"al1": "Turgeon",
"ai2": "W. G.",
"al2": "Lyons",
"oau": "P. Mikkelsen, G. Rosenberg, F. Moretzsohn",
"eds": "D. L. Felder, D. K. Camp",
"pbt": "Gulf of Mexico–Origins, Waters, and Biota. Biodiversity",
"pbl": "Texas A&M Press",
"pgf": "711",
"pgl": "744",
"lan": "English"
}

Compendium

Should go under book

{
"oid": "ref:59400",
"pty": "compendium",
"tit": "Malacolog 4.1.1: A Database of Western Atlantic Marine Mollusca",
"pby": "2009",
"ai1": "G.",
"al1": "Rosenberg",
"pbt": "www.malacolog.org",
"lan": "English"
}

Guidebook

Should go under Book

{
"oid": "ref:40884",
"pty": "guidebook",
"tit": "Mollusca: Fort Thompson Formation (Late Pleistocene)",
"pby": "2010",
"ai1": "B. A.",
"al1": "Kittle",
"ai2": "R. W.",
"al2": "Portell",
"pbt": "Florida Fossil Invertebrates",
"vol": "12",
"pgf": "1",
"pgl": "32",
"lan": "English"
}

Journal Article

Journal article

{
"oid": "ref:18615",
"pty": "journal article",
"tit": "Maastrichtian inoceramid bivalves from Central Chiapas, southeaster México",
"pby": "2006",
"ai1": "G.",
"al1": "Alencáster",
"ai2": "L.",
"al2": "Omaña",
"pbt": "Journal of Paleontology",
"vol": "80",
"vno": "5",
"pgf": "946",
"pgl": "957",
"lan": "English",
"doi": "10.1666/0022-3360(2006)80[946:mibfcc]2.0.co;2"
}

M.S. Thesis

Book

{
"oid": "ref:84455",
"pty": "M.S. thesis",
"tit": "Análise cladíistica dos bivalves do Grupo Passa Dois (Neopermiano), Bacia do Paraná, Brasil: implicações taxonômicas, evolutivas e paleobiogeográficas",
"pby": "1999",
"ai1": "L. H. C.",
"al1": "Mello",
"pbl": "IGc-Universidade de São Paulo",
"pgf": "1",
"pgl": "160",
"lan": "English",
"doi": "10.11606/d.44.1999.tde-05102015-131815"
}

Ph.D. Thesis

Book

{
"oid": "ref:9529",
"pty": "Ph.D. thesis",
"tit": "Taxonomy and palaeoecology of the benthic macroinvertebrate fauna from the Middle Jurassic of northwestern Jordan",
"pby": "1998",
"ai1": "F.",
"al1": "Ahmad",
"lan": "English"
}

Serial Monograph

We feel that this should go under book. We noticed though that the PBOT book doesn't handle this case well. This actually might need a new PBOT publication type

{
"oid": "ref:11610",
"pty": "serial monograph",
"tit": "Upper Cretaceous of the Pacific Coast",
"pby": "1958",
"ai1": "F. M.",
"al1": "Anderson",
"pbt": "Geological Society of America Memoir",
"vol": "71",
"pgf": "1",
"pgl": "378",
"lan": "English",
"doi": "10.1130/mem71-p1"
}