Update README and rename directories in line with new terminology

[gaurav]

Since the name and role of this repository has changed (#19), we no longer refer to these as testcases but as PHYX files. I've updated the README file to reflect this (closes #30) and renamed some of the directories in this repository to make their purpose clearer, as well as cleaning out some out-of-date information that no longer needs to be stored outside the PHYX file itself. Individual lists of phyloreferences have been removed, and will eventually be replaced by an automatically generated table that provides information on the types of included phyloreferences (#34).

[hlapp]

See comment about license. We should fix this.

[hlapp]

Where's the Apache license coming from?? OBO recommends CC-BY. I would suggest CC0, unless we have good arguments as to why we cannot waive copyright (for example, because someone other than us has it), or why our terms of reuse have to include a legal requirement for attribution (as opposed to a scientific norm mandating proper citation).

[gaurav]

The Apache license is intended to apply to the software in this repository -- the phyx2owl script and the testing scripts -- which is clearly not what the text in the README file says. I've updated the README file to clarify that, and added a copy of the CC0 legal code into the phyx directory to make it clear that a separate license applies there.

As for the question of other authors' copyright, I don't think you could argue that the phylogeny (which is a series of assertions) or the raw phyloreference (which is a list of specifiers) count as creative works, so CC0 sounds great to me. We are currently recording information that helps to explain why the clade was defined in a particular way (e.g. "Because sister group relationships are better resolved and supported than basally-branching ingroup relationships within this clade, a branch-modified node-based definition was used to maximize definitional and compositional stability (Cantino et al., 2007).", see reference below). This is arguably copyrightable, but I think it's small enough that we could argue fair use or remove it on a case-by-case basis if there are specific complaints.

clade-ontology/testcases_too_slow/Wojciechowski, 2013/paper.json

Line 74 in 187c78c

"cladeDefinition": "Papilionoideae (L.) DC. [M. F. Wojciechowski], converted clade name.\n\nDefinition (branch-modified, node-based): The most inclusive crown clade containing Castanospermum australe A. Cunn. ex Mudie 1829 and Vicia faba L. 1753 but not Caesalpinia gilliesii (Wall. ex Hook.) D. Dietr. 1840, Gleditsia triacanthos L., or Dialium guianense (Aubl.) Sandwith 1939. Because sister group relationships are better resolved and supported than basally-branching ingroup relationships within this clade, a branch-modified node-based definition was used to maximize definitional and compositional stability (Cantino et al., 2007).\n\nComments on name. Papilionoideae (L.) DC. 1825 is a preexisting scientific name established under the rank-based ICBN and applied to the subfamily of the Leguminosae Jussieu 1789 that corresponds to this clade. Faboideae Rudd 1968 is an alternative name for this subfamily of Fabaceae Lindl. 1836 or Leguminosae, whereas the similar Papilionaceae Giseke 1792 is the appropriate name for this taxon when the subfamily is treated as a separate family from the Caesalpiniaceae R. Br. 1814 and Mimosaceae R. Br. 1814.\n\nReference phylogeny: Cardoso et al. (2012; Fig. 1). The monophyly of Papilionoideae has been demonstrated in all higher-level molecular phylogenetic analyses published to date beginning with Käss and Wink (1996) and Doyle et al. (1997), albeit sometimes without robust statistical support. Later analyses such as Wojciechowski et al. (2004;Fig. 2) and Cardoso et al. (2012; Fig. 3) have provided unequivocal, robust support for this clade.\n\nDiagnostic apomorphy: Flowers generally zygomorphic, or some actinomorphic, adaxial petal generally outside the adjacent lateral petals, sepals generally united at base.\n\nComposition: This clade, comprised of more than 478 genera and 13,800 species (Lewis et al., 2005), is cosmopolitan in distribution and includes the vast majority of agriculturally important legumes such as Pisum sativum L. (pea), Medicago sativa L. (alfalfa), Trifolium L. (clovers), Vicia L. (vetches), Lens Mill. (lentils), Lupinus L. (lupins), Glycine max (L.) Merr. (soybean), Phaseolus L. (beans), Lablab purpureus (L.) Sweet (hyacinth bean), and Arachis hypogaea L. (peanut).\n\nSynonyms/Etymology: Papilionoideae (L.) DC. 1825, Faboideae Rudd 1968, and the informal name “Papilionoids”. The name “papilionoid” most likely comes from the resemblance of the typical or characteristic flower to a butterfly (papilio, from Latin), especially when the flower is dissected into its component five petals.",

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[hlapp]

So fair use permitting us to reuse the definition texts here does not mean they are in the public domain, and fair use does mean you can claim intellectual property rights. So I'm skeptical that we have the rights to release the clade definition texts into the public domain.

Maybe this needs some consultation first with corresponding experts. Given the legal uncertainty, I'd argue we cannot at this point attach a CC0 waiver if the definition texts are included, because once we do we've waived our rights and we can't just take that back.

[gaurav]

@hlapp I've tried to improve the licensing situation to distinguish between Apache licensed software (e.g. phyx2owl and the testing scripts) and the CC0 licensed ontology (the PHYX file and, eventually, the ontology), and fixed the obviously wrong text in the README file. Let me know if there are any additional changes I should make!

[hlapp]

So fair use permitting us to reuse the definition texts here does not mean they are in the public domain, and fair use does mean you can claim intellectual property rights. So I'm skeptical that we have the rights to release the clade definition texts into the public domain.

Maybe this needs some consultation first with corresponding experts. Given the legal uncertainty, I'd argue we cannot at this point attach a CC0 waiver if the definition texts are included, because once we do we've waived our rights and we can't just take that back.

[hlapp]

So fair use permitting us to reuse the definition texts here does not mean they are in the public domain, and fair use does not mean you can claim intellectual property rights. So I'm skeptical that we have the rights to release the clade definition texts into the public domain.

Maybe this needs some consultation first with corresponding experts. Given the legal uncertainty, I'd argue we cannot at this point attach a CC0 waiver if the definition texts are included, because once we do we've waived our rights and we can't just take that back.

[ncellinese]

Yes, totally agree with this. nico

…

On Jun 22, 2018, at 10:25 AM, Hilmar Lapp ***@***.***> wrote: So fair use permitting us to reuse the definition texts here does not mean they are in the public domain, and fair use does mean you can claim intellectual property rights. So I'm skeptical that we have the rights to release the clade definition texts into the public domain. Maybe this needs some consultation first with corresponding experts. Given the legal uncertainty, I'd argue we cannot at this point attach a CC0 waiver if the definition texts are included, because once we do we've waived our rights and we can't just take that back. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACaXwRwl6nUA51VlKUNhZ_JaDhoB8EfNks5t_P5mgaJpZM4UsYCZ>.

[hlapp]

I'd suggest that for the README we move all URLs to the end. It makes for much better reading, IMHO.

[hlapp]

My feeling is we should standardize on a "default" software license, because I don't see much point in having different licenses for different pieces of software we develop, given that we're not defaulting on the GPL, which we may otherwise have reason to relax from depending on the specific tool or code.

So are you suggesting the Apache 2.0 license as our default, and do you have reasons to choose it over, say MIT, or BSD2/3, as the most commonly used "permissive" licenses.

[gaurav]

Actually, it looks we've standardized to the MIT license across all Phyloref software products as we decided to in phyloref/phylo2owl#1 -- except for the Clade Ontology, which ended up with the Apache License before we'd closed that issue. I've now relicensed it with the MIT license in 5e1ec27.

[gaurav]

I've moved all the links to the bottom of the README file and replaced the Apache license with an MIT license to bring it in line with all the other Phyloref software products. Let me know what you think!

[hlapp]

Looks good!