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Superconductors material dataset

License: Apache License 2.0

Python 9.78% Jupyter Notebook 90.22%
material-informatics text-mining tdm superconductors

supermat's Introduction

Documentation Status Build unstable

SuperMat

SuperMat (Superconductors Material) dataset is a manually linked annotated dataset of superconductors related materials and properties.

Content

Feel free to contact us for any information.

Reference

If you use the data, please consider citing the related paper:

@article{doi:10.1080/27660400.2021.1918396,
   author = {Luca Foppiano and Sae Dieb and Akira Suzuki and Pedro Baptista de Castro and Suguru Iwasaki and Azusa Uzuki and Miren Garbine Esparza Echevarria and Yan Meng and Kensei Terashima and Laurent Romary and Yoshihiko Takano and Masashi Ishii},
   title = {SuperMat: construction of a linked annotated dataset from superconductors-related publications},
   journal = {Science and Technology of Advanced Materials: Methods},
   volume = {1},
   number = {1},
   pages = {34-44},
   year  = {2021},
   publisher = {Taylor & Francis},
   doi = {10.1080/27660400.2021.1918396},

   URL = { 
           https://doi.org/10.1080/27660400.2021.1918396
   },
   eprint = { 
           https://doi.org/10.1080/27660400.2021.1918396   
   }
}

Usage

Getting started

To use the scripts and analysis data

conda create --name SuperMat pip
pip install -r requirements.txt 

Conversion tools

python scripts/tsv2xml.py --help

Analysis tools

The analysis tools provide statistics and information from the dataset, they also run consistency checks of the format and content. Results can be seen directly on the repository.

jupyter-lab

Annotation guidelines

We use reStructured TExt using the utility Sphinx which provide several output formats. Currently we support XML and PDF.

To build this documentation locally, we recommend to create a virtual environment such as virtualenv or conda:

conda create -name guidelines 
conda activate guidelines
conda install sphinx

Build HTML site

To build the documentation as a website:

sphinx-build -b html docs _build

Automatic build

Sphinx allows automatic build using sphinx-autobuild, which will automatically reload and update on a webservice spawned at-hoc. You can launch the automatic build using:

sphinx-autobuild docs build_

you can access the service by opening the browser at http://localhost:8000.

Build PDF

You can export this document as PDF using rst2pdf.

Even if you have conda, you should install the version provided by pipy:

pip install rst2pdf

Then you need to modify your config.py by adding the following information:

extensions = ['rst2pdf.pdfbuilder']
pdf_documents = [('index', u'filename', u'Title', u'Author')]

and build using

sphinx-build -b pdf sourcedir builddir

and a file with the specified name will be created in builddir.

Make a new release

bump-my-version bump major|minor|patch 

Licence

The dataset is licensed under CC BY 4.0 CC. The Bibliographic data refers to the original content.

The code is licences under Apache 2.0

supermat's People

Contributors

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Watchers

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supermat's Issues

me_methods: 'ac susceptibility and dc resistance'

Here an example:

Superconducting transitions measured by ac susceptibility and dc resistance.

what should be annotated as <me_method>?

Superconducting transitions measured by <me_method>ac susceptibility</me_method> and dc <me_method>resistance</me_method>.

I'm wondering whether ac and dc are also to be included in the annotation

Ref: SSC1310125-CC.superconductors.tei.xml.tsv

Inconsistency second round of annotations

Hi,
I've got these inconsistencies I'm not sure about:

image

and

image

except for sulfur hydride, which in Drodzov paper is used for both class and material, what do you think about the rest?

post-correction validation

We need to confirm the following modification (left: before, right: after)

  • L089147002
    image

  • Tanaka et all
    image
    image

  • P068132507
    image

  • P068214517
    image

  • P072014504
    image
    image
    image
    image
    image
    image

  • PCS2739
    image

15 In-NQR measurements

In summary, we have presented the unique characteristics of superconductivity and its relation to antiferromagnetic spin fluctuations in the heavy- fermion superconductor CeIrIn 5 through 115 In-NQR measurements under pressure.

need confirmation that is not a measurement method

What do you think?

CF: L094037007-CC.superconductors

nematic superconductivity, what is that?

I'm wondering what "nematic superconductivity" means...

here what I found about nematic: Whose molecules align in loose parallel lines.

but, in practice, what does that means? is that information useful?

Missing annotations?

Hi there,

I'd like to use this task as part of an evaluation suite for a chemistry-specific natural language model. Other than the SuperMat-1.0.csv file in data/csv I'm not seeing where the annotations are being stored. In the paper you refer to an annotated structure within the xml files, however I'm not seeing any data within the text nodes for any of the xml files you've included in the repo. Am I missing or misunderstanding something?

Screen Shot 2021-11-15 at 12 27 05 PM

epitaxial as a modifier?

In this example: Growth and superconducting transition of Pr 1−x Ca x Ba 2 Cu 3 O 7−δ (x ≈0.5) epitaxial thin films

do you agree on annotating: Growth and superconducting transition of <material>Pr 1−x Ca x Ba 2 Cu 3 O 7−δ (x ≈0.5) epitaxial thin films</material>

or just the material formula, as epitaxial does not mean anything important?

Growth and superconducting transition of <material>Pr 1−x Ca x Ba 2 Cu 3 O 7−δ (x ≈0.5)</material> epitaxial thin films

CF: SST0180041-CC.superconductors.tei.xml

Sentence combining AF fluctuation and doping range

I have some doubt about this sentence:

The rise of T c without AF fluctuations was observed only for x = 0.14 (see the dashed arrow in Fig. 4), because AF fluctuations remain in a lower doping range than x = 0.14 and unfortunately x = 0.14 is nearly the highest level of F doping.

we have discussed it but I forgot what was told. Could someone explain below? What should be annotated?

Can someone advice?

List of materials listed in the sample preparation - annotate or not?

The starting materials, Co 3 O 4 , SrCO 3 , Y 2 O 3 , CaCO 3 and CuO, were mixed to nominal ratios and calcined at 975 o C and 1000 o C with an intermediate [..]

What did we said about the materials that are used for composing the output material?

In this case, as the substrate, we should ignore them unless there is a specific reference to Tc or tcValue. What do you think?
Alternative is that we keep them annotated and we figure them out afterwards

CF: SSC1270493-CC.superconductors.tei.xml.tsv

variation of Tc

I think in the sentence variation of Tc, only Tc should be annotated because variation does not provide any useful information (is increasing, is decreasing?)

material name variations

Here an example:
Another example, in this sentence `a) and (b), the critical transition temperature of 150 nm thick Ba122 :Co films grown on MgO substrates were T onset c = 20 K.

I think material should be annotated the whole descriptive name: 150 nm thick Ba122 :Co films grown on MgO substrates

any idea?

class or material?

Here two examples from the same paragraph:

The substitution of Pr in R-123 (R = rare earth) and [...]

The Pr-substituted R-123 compounds also [...]

right now R-123 is annotated as class.

I'm wondering if instead we should annotate substitution of Pr in R-123 as a material?
What do you think?

CF: SSC1280097-CC.superconductors.tei.xml.tsv

is NMR a measurement method?

as previously discussed it seems NMR is not a measurement method, but it has been annotated as such. j

what is the final decision?

when do and do not annotate <pressure>?

There is one sentence I want to amend in the guidelines:

any pressure that is not “critical” or linkable to a critical temperature, should be ignored ...

I want to change it to

any pressure that is not “critical” should be ignored

so that any pressure that is critical, although not linkable should be therefore annotated

The reason is to increase the amount of annotations in output which are still relevant, although not linked with our current rules.

CF: supercon/L089157004-CC.superconductors.tei.xml.tsv

Zero-field measurements is a <me_method>?

Zero-field measurements indicate no static magnetic fields developing below the transition temperature.

Annotate or not?

CFR: L089147002-CC.superconductors.tei.xml.tsv

the binary compound M 5 X 3

Increasing research interest has emerged lately on the binary compound M 5 X 3 (M=alkaline earth or transition metal, and X=main group elements including Al, Si and As families), which includes superconductivity , ferro/antiferromagnetism , host-interstitial chemistry , and high temperature structural applications .

M 5 X 3 looks like a material to me, could you please confirm it's a class?

CF: Li_2018_Supercond._Sci._Technol._31_085001.superconductors.tei.xml

Complex substitutions / Dopants as material names

Question from @a017731

I have a question I will leave it here later

Image_Pasted_at_2020-5-18_11-02

Some Tc Values were missed.
However please note that it says 3.3K for Cs, 6.3K For Rb and 9.6 K for K
That means is 3.3 K for CsO2O6
Now my question is, do we tag cs rb and K as materials and link to it
or we link to AOs2O6 (A= Cs, Rb, K)?

Reference supercon-batch-1/L095167004-CC.superconductors.tei.xml.tsv

Measurement method aggregation

I've computed this, by aggregating measurement methods value together. The principle is very simple, I search for values contained in "names" and aggregate them:

  "specific heat": {
        "names": ["heat", "therm"]
    }, 
    "magnetic susceptibility": {
        "names": ["susceptibilit"]
    }, 
    "resistivity": {
        "names": ["resistivit", "resistance", "electrical"]        
    },
    "magnetisation": {
        "names": ["magneti"]        
    },
    "empirical calculation": {
        "names": ["calcula", "predict", "theor"]        
    }

Could you please confirm that "magnetisation" and "magnetic susceptibility" two different measurement methods? I have a doubt and is not mentioned in the guidelines (http://falcon.nims.go.jp/superconductors-documentation/guidelines.html#measurement-methods

Here is what I obtain

image

Do you have any comment on that? Does it looks reasonable?

R-123 vs La-123

here a sentence: Since the starting model was assumed to be an R-123 tetragonal structure, the LaPrCaBCO (x = 0.1 -0.5) were normalized to La-123 .

Would be correct to have R-123 as class and La-123 as material?

R-123 represent the system and La is the replacement for it? Like we could have Cu-123?

CFR: SSC1280097-CC.superconductors.tei.xml

are 82K and 56K this critical temperatures?

Since STM is a local probe, there is a possibility that it does not reflect the 
bulk T c of the sample  and therefore it is important to consider the energy gap magnitude. 
Both refs. and present energy gaps in the range 35-40 meV in addition to the  pseudogap behavior. 

This gap magnitude is consistent with optimally doped or slightly overdoped samples and 
thus the doping level at the junction is  not well established. In a more recent study, SIS 
break junctions of underdoped and overdoped Bi-2212 with T c = 82 K were fabricated using an  
STM by M. Oda et al. . 
Both sets of data exhibited a pseudogap above T c ; however, the overdoped tunneling conductance 
showed a smaller gap which  fills in at a much lower temperature than underdoped and thus T * is 
closer to T c . Taken together the tunneling studies have established that the  pseudogap persists 
with overdoping down to T c = 82 K , but is absent when T c = 56 K .  

A natural question might be whether there is any change in the pairing symmetry associated with 
the loss of a pseudogap. One may assume that  increasing hole doping makes the Bi-2212 normal-state 
more Fermi-liquid-like, leading possibly to an s-wave BCS superconductor. There are ARPES  observations 
that suggest s-wave BCS behavior in the heavily overdoped phase . However, the tunneling subgap 
conductance shapes at low  temperatures in figs. 1(a) and (b) are not consistent with the s-wave 
BCS theory prediction which is supposed to be flat near zero bias. Here what we  observed is that 
the d-wave-like subgap structure persists at the T c = 56 K

There is 82k and 56k, which are noted as Tc = but... are them critical temperatures?

CF: supercon/EPL0580589-CC.superconductors.tei.xml.tsv

resistivity -> always me_method?

In one of the previous meetings, there was a question raised from Terashima-san, about the resistivity which is always annotated as me_method.

Here some examples:

  1. Although the <me_method>resistivity</me_method> measurements reported in Ref. were made with contact [...]
  2. <p>Temperature-dependent <me_method>resistivity</me_method> of <material>polycrystalline WB 4.2</material> measured from 300 to 1.7 K [...]
  3. On cooling, we see signatures of superconductivity: a sharp drop of the <me_method>resistivity</me_method> to zero and a decrease [...]

We agreed to keep annotating it but the rules here are a bit weak.

I've been thinking a bit more

  1. we annotate resistivity only when the paper is talking about the method of measuring the Tc
    • we need to clarify all various cases
    • we need to re-check all previous annotations
  2. we keep the rule a bit loose and annotate as we have been done until now

Any though?

Review of material modifiers

Question from @a018044:

Example 1:
image

How many modifiers should be annotated as material?

Example 2:
image

Crystal to be annotated or not?

Comment from @a017731

I dont think so. Well maybe it can be equivalement of 'bulk', but for me is ambiguous if he is saying its a single or poly crystal

probably related to #26

Substrate

The sample under study is plated with a conventional low T c superconductor, in this case an Al film.

Al film is a substrate, right?

therefore we should not annotate, according to https://gitlab.nims.go.jp/lfoppiano/superconductors-documentation/issues/12#note_34835 and guidelines:

If the substrate is adjacent to the material (e.g. blablabla/StRO3), 
the whole sequence should be annotated as <material> but if the substrate 
is apart from the material name should be ignored.

CRF: supercon/APL0774202-CC.superconductors.tei.xml.tsv

doping rate with variables, as list of values

When a material is presented just the doping ratio with one variable and several values, we annotate all as a single annotation, e.g x = 0.01, 0.2 and so on and we link it to each of the tc value that are referenced:

Example: The Tc for x = 1,2,3,4 is 3K, 4K, 5K and 6K respectively

Annotate x = 1,2,3,4 as one annotation and each tc separately and link them

To be added in the guidelines

Andreev critical temperature

I found this reference Andreev critical temperature with TAc. Does this classify as critical temperature?

Example:
For this reason, in all the contacts, we therefore carefully studied the temperature dependence of the conductance in order to determine the critical temperature of the junction, i.e. the 'Andreev critical temperature', T A c . In an overall of 35 different contacts, T A c was found to be 11.3 ± 0.1 K, in best agreement with the bulk T c 's of the samples and in contrast with a previous report .

L093156802-CC.superconductors

atomic structure is a modifier?

In the guidelines we have stated that Modifiers can be (http://falcon.nims.go.jp/superconductors-documentation/guidelines.html#material-name):

  • pure, overdoped etc...
  • wafer, film, etc...
  • in #13 we decided to add epitaxial

Can we consider also the atomic structure a modifier, for example:

These M 5 X 3 phases are found crystallized in several different unique crystal systems, namely; hexagonal Mn 5 Si 3 -type , tetragonal Cr 5 B 3 and W 5 Si 3 -type , and orthorhombic Nb 5 As 3 and Y 5 Bi 3 -type structures. Often, one compound might crystallize into two different structures, one as a high temperature phase and the other as a low temperature phase.

we have tetragonal, orthorhombic etc...

What do you think?

CFR: supercon/Li_2018_Supercond._Sci._Technol._31_085001.superconductors.tei.xml.tsv

Inconsistencies from analysis

Currently, we have the following inconsistencies (I analysed batch 1 (before the latest correction, which is still ongoing), 2, 3 and 4):

image

  1. 0, 7 and 8 are obvious
  2. 3 has been answered in #46 -> class
  3. 2 is discussed in #48 (please answer there)
  4. 5 and 6 is discussed in #49
  5. 1 was already discussed in the past
  6. 4 I corrected Co oxide is a <class> based on previous discussions

material formula for expressing structure

I have some questions regarding one paper which uses strange reference for structure

These M 5 X 3 phases are found crystallized in several different unique crystal systems, namely; hexagonal Mn 5 Si 3 -type , tetragonal Cr 5 B 3 and W 5 Si 3 -type , and orthorhombic Nb 5 As 3 and Y 5 Bi 3 -type structures. Often, one compound might crystallize into two different structures, one as a high temperature phase and the other as a low temperature phase. For example, this is seen in both Ta 5 Ge 3 and Nb 5 Si 3 compounds. Chemical/interstitial doping was also found to be able to change the crystal structures upon doping, in turn, tuning the physical properties of the host binaries by the nature and amount of interstitial atoms that could be introduced.

In this sentence there are some material that are cited as type structure: exagonal Mn 5 Si 3 -type , tetragonal Cr 5 B 3 and W 5 Si 3 -type , and orthorhombic Nb 5 As 3 and Y 5 Bi 3 -type structures.

  1. I wonder if these annotation should be removed. If we keep them the rule say we should include the structure as well.

Later in the paper the author writes Superconductivity has been reported firstly in Zr 5 Sb 3 with T c ∼2.3 K , and later in the Ru-doped Zr 5 Sb 3 and Hf 5 Sb 3 (with structure changing from Mn 5 Si 3 type to W 5 Si 3 type upon doping).

  1. in this sentence do you understand that Ru-doped Zr 5 Sb 3 has the same Tc as the Zr 5 Sb 3 (non-doped)?
  2. the following sentence: with structure changing from Mn 5 Si 3 type to W 5 Si 3 type upon doping I wonder if these are just references to the structure types and should not be annotated.

paper: Li_2018_Supercond._Sci._Technol._31_085001

type-II Dirac semimetal PdTe2 - PdTe2 should be included?

[...]Though the superconducting phase of the type-II Dirac semimetal PdTe2 was shown to be conventional in nature,[...]

We annotate type-II Dirac semimetal as

Should we:

  1. annotate PdTe2 within the same label (<class>)
  2. annotate PdTe2 as <material>
  3. annotate PdTe2 as <sample>
  4. annotate type-II Dirac semimetal PdTe2 as <sample>

?

diboride / borocarbide can be considered classes?

Perhaps this question is a bit silly... I have a small doubt:

Example 1: [...] the magnesium diboride ( MgB 2 ) the archetype [...]

Example 2: [...] nickel borocarbide YNi 2 B 2 C [...]

We decided not to annotate magnesium diboride as material, as the formula takes priority. Should I annotate diboride as class? In the second case, can we apply the same rule ("borocarbide" as class) or we do not annotate at all?

β-pyrochlore oxide

Example: [..]on all the three members of the β-pyrochlore oxide superconductors. β-pyrochlore oxide was annotated as

See another sentence:
A new family of transition metal oxide superconductors AOs 2 O 6 (A = Cs, Rb, K) called β-pyrochlore oxides was found recently [1-4].

According to the new rules, we should annotate oxide as class but might be too generic, so β-pyrochlore oxide is a class or material?

CF: L095167004-CC.superconductors.tei.xml.tsv

Tc expression strategy

Tc expressions are currently annotated without any modifier, such as higher, high etc..

Point was made about the importance of the information related to the critical temperature, in particular whether is a relative value (higher than), an absolute value (higher) and so on.

Expand the me_method to certain instruments/tecniques?

Question from @a017731

image

In this example, it is clear that the value was measured by magnezation. However I had to tag 'SQUID magnetometer' as me_method
In this case its actually the equipment used to perform, but there was no other option. Suggestions?

Questions about the <material> (and <class>) tag

The and annotations are overlapping:

Here some point / discussions:

  • Discussion 1

supercon/L087187001-CC.superconductors.tei.xml.tsv: metallic pyrochlore oxide is it a class or a material?

You have 1) We make the first report that a metallic pyrochlore oxide Cd 2 Re 2 O 7

and 2) A large number of compounds are classified in the family of pyrochlore oxides

which looks like material the first and class the second

Mattermost

  • Discussion 2

image

In case we have time to discuss tomorrow, let me put a question. In the above screenshot, it is saying that Pr0.5Ca0.5Ba2Cu3O7-d thin films grown on STO substrate has tc0 of 35.6 K. Pr0.5Ca0.5Ba2Cu3O7-d thin films grown on YSZ substrate has tc0 of 37 K. It might be difficult for machine now to link it properly, I guess.
23:25

Here is another similar expression

image
At most we can do right now is, like here, link Pr0.5Ca0.5Ba2Cu3O7-d with tcvalues, ignoring substrates. But if we could involve the additional conditions such as "grown on STO" in future, it would be better.

Mattermost

  • Discussion 3

Maybe this can be verified in the coming meeting, but here let me note. It is about the definition of class and material. To me, it sound nice that we call class when it contains several materials, and individual material composition (combination of atoms) is difficult to specify.
For instance, "Fe-based 122" is a class, since we cannot immediately specify what we have other than Fe atom

Mattermost

  • Discussion 4

Example here:
image

We discussed and agreed that material_formula (abbreviation) goes in a single <material> annotation. What about this case?
Should both be considered materials? class/materials?

Mattermost

New possible measurement methods?

Example 1: <me_method>Magnetic field penetration depth</me_method> λ and high-pressure studies traditionally play an important role in superconductivity.

Example 2: we performed <me_method>DC-magnetization measurements</me_method>

Are these the measurement method that we have seen as "magnetic susceptibility"?

CF: L093157004-CC.superconductors

class name, how to choose?

This is related to #28.

Given the following example:
We report transverse field and zero field muon spin rotation studies of the superconducting rhenium oxide pyrochlore, Cd2Re2O7.

What part of the string rhenium oxide pyrochlore should I annotate as class?
rhenium oxide pyrochlore
oxide pyrochlore
pyrochlore
pyrochlore and oxide
rhenium oxide

or something else?

CRF: L089147002-CC.superconductors.tei.xml.tsv

Strange class name, is it really a class?

image

See the MmA2Qn-1CunOm+2+2n±δ (M-m2(n-1)n; category-A) and MmA2kBsCu1+kOm+4k+2s±δ (M-m(2k)s(1+k); category-B) ... this has been annotated as class... is it really a class?

CF: SSC1270493-CC.superconductors.tei.xml.tsv

Material or class?

Reviewing the last data, I found two inconsistencies between material and class:

  1. La-214

Examples:

Therefore, they have proposed that the dynamical stripe correlations, observed in a wide range of hole concentration in the <class>La-214</class> superconductors, are pinned by the TLT structure, leading to the appearance of the static stripe order and [...]

There could be seen Bragg peaks of the <class>La-214</class> phase and no impurities such as <material>La 1+x Ba 2−x Cu 3 O 7−δ</material> [...]

The origin of the sign reversals in S ab and R H is not clarified, but it is considered that these behaviors are characteristic of the 1/8 anomaly in a series of <class>La-214</class> systems.

CFR: P064144524-CC.superconductors.tei.xml

  1. Ru-2122

Examples:

<p>In the <material>Ru-2122</material> system, the W-FM state, as well as irreversibility phenomena

The qualitative model of the magnetic structure in the <material>Ru-2122</material> system is discussed.

There is no evidence for super-cell peaks in the <material>Ru-2122</material> samples.</p>

The exact nature of the local structural distortions causing DM exchange coupling in <material>Ru-2122</material> (see above) is not presently known.

CFR: P066024503-CC.superconductors.tei.xml

Correction to the guidelines

Tc expressions -> basic rules:

relative information attached to critical temperature should be annotated, for example: increasing Tc, raising Tc, etc.. only when the value they refer to is absolute.

After discussion the statement only when the value they refer to is absolute. is not necessary for these reasons:

  1. many tc expressions of this kind are not followed by a tcValue
  2. it is still important to know when there are fluctuation of tc even if the referenced value is relative (it will not be annotated, anyway).

See change: 9194dbf7d7f4ee5ca09259aa1659f3cdadbdef05

Transition temperature / Critical temperature

Just a clarification.

The term "transition temperature" looks, to me, very generic. Is there a general definition or it's just a temperature where anything happens?

For example in this sentence TLO and TLT are not Tc, right?

[...] two structural phase transition temperatures are determined as T LO =90 K and T LT =65 K in La 1.84 Y 0.04 Sr 0.12 CuO 4. T LO is the structural phase transition temperature to the low-temperature orthorhombic (OLT) phase, and T LT is that to the low-temperature tetragonal (TLT) phase. [...]

SQUID Magnetometer

As discussed in the meeting, to be sure I don't forget, SQUID Magnetometer is not a measurement method but an equipment, therefore should not be annotated as <me_method>.

Should measurement_method be linked to the tcValue

The question is originated by the fact that certain measurement method can result in different tcValue.

However:

  • me_method might be located distantly from the tcValue
  • tcValues linkable to different me_method are not so frequent

The decision, for the time being is to not link me_method to tcValue

Overlapping annotations

Question from @a017731:

Image_Pasted_at_2020-5-18_11-30

Do we tag zero resistivity transition as Tc or only resistivity as me_method

Reference: supercon-batch-1/Liu_2018_Supercond._Sci._Technol._31_125011.superconductors.tei.xml.tsv

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